"It's called overamping": experiences of overdose among people who use methamphetamine.

BACKGROUND: The USA is experiencing increases in methamphetamine use and methamphetamine-related or attributed deaths. In the current study, we explore qualitative narratives of methamphetamine overdose and strategies used by people who use drugs to reduce the undesirable effects associated with methamphetamine use. METHODS: We conducted 21 qualitative interviews with people over the age of 18 who reported using methamphetamine in the previous 3 months in Nevada and New Mexico. Interviews were recorded, transcribed, and analyzed using qualitative thematic analysis. RESULTS: Respondents described a constellation of psychological and physical symptoms that they characterized as "overamping," experienced on a continuum from less to more severe. Reports of acute, fatal methamphetamine overdose were rare. Few reported seeking medical attention for undesirable effects (usually related to psychological effects). General self-care strategies such as sleeping and staying hydrated were discussed. CONCLUSIONS: When asked directly, our respondents claimed that acute, fatal methamphetamine overdose is rare or even impossible. However, they described a number of undesirable symptoms associated with overconsumption of methamphetamine and had few clinical or harm reduction strategies at their disposal. Addressing this current wave of drug-related deaths will require attention to the multiple factors that structure experiences of methamphetamine "overdose," and a collaborative effort with PWUDs to devise effective harm reduction and treatment strategies.

Incidence of RNA viruses infecting taro and tannia in East Africa and molecular characterisation of dasheen mosaic virus isolates.

Taro (Colocasia esculenta) and tannia (Xanthosoma sp.) plants growing in 25 districts across Ethiopia, Kenya, Tanzania and Uganda were surveyed for four RNA viruses. Leaf samples from 392 plants were tested for cucumber mosaic virus (CMV), dasheen mosaic virus (DsMV), taro vein chlorosis virus (TaVCV) and Colocasia bobone disease-associated virus (CBDaV) by RT-PCR. No samples tested positive for TaVCV or CBDaV, while CMV was only detected in three tannia samples with mosaic symptoms from Uganda. DsMV was detected in 40 samples, including 36 out of 171 from Ethiopia, one out of 94 from Uganda and three out of 41 from Tanzania, while none of the 86 samples from Kenya tested positive for any of the four viruses. The complete genomes of nine DsMV isolates from East Africa were cloned and sequenced. Phylogenetic analyses based on the amino acid sequence of the DsMV CP-coding region revealed two distinct clades. Isolates from Ethiopia were distributed in both clades, while samples from Uganda and Tanzania belong to different clades. Seven possible recombination events were identified from the analysis carried out on the available 15 full-length DsMV isolates. Nucleotide substitution ratio analysis revealed that all the DsMV genes are under strong negative selection pressure.

ICTV Virus Taxonomy Profile: Nanoviridae.

Nanoviridae is a family of plant viruses (nanovirids) whose members have small isometric virions and multipartite, circular, single-stranded (css) DNA genomes. Each of the six (genus Babuvirus) or eight (genus Nanovirus) genomic DNAs is 0.9-1.1 kb and is separately encapsidated. Many isolates are associated with satellite-like cssDNAs (alphasatellites) of 1.0-1.1 kb. Hosts are eudicots, predominantly legumes (genus Nanovirus), and monocotyledons, predominantly in the order Zingiberales (genus Babuvirus). Nanovirids require a virus-encoded helper factor for transmission by aphids in a circulative, non-propagative manner. This is a summary of the ICTV Report on the family Nanoviridae, which is available at ictv.global/report/nanoviridae.

Factors Associated With Calling 911 for an Overdose: An Ethnographic Decision Tree Modeling Approach.

Objectives. To identify factors that influence when people who use drugs (PWUDs) call 911 for an overdose. Methods. We conducted 45 qualitative interviews and 180 surveys with PWUDs who had recently witnessed overdoses in Southern California from 2017 to 2019. We used conditional inference tree and random forest models to generate and validate a model to predict whether 911 would be called. Results. Our model had good in- (83%) and out-of-sample (84%) predictive accuracy. Three aspects of the social and policy environment influenced calling 911 for an overdose: the effectiveness of response strategies employed, the behavior of other bystanders, and whether the responder believes it is their responsibility to call. Conclusions. Even in the presence of policies that provide some protections, PWUDs are faced with difficult decisions about calling 911 and must weigh their own safety against that of an overdose victim. Potential interventions include strengthening training and safety planning for PWUDs, bolstering protections for PWUDs when they call 911, and separating law enforcement response from emergency medical response to overdoses.

Production of selectable marker gene-free Cavendish banana (Musa spp.) using a steroid-inducible recombinase platform.

Genetic improvement of commercially accepted banana cultivars is strongly reliant on the ability to introduce genes that encode important agro-traits such as disease resistance. In most cases this can only be achieved using a transgenic approach. Public and regulatory acceptance of these events would greatly increase with "clean" single copy integration events free of the selectable marker gene and extraneous vector backbone. This would also allow for the successive addition of new genes and traits as they become available. In this study, we used the pMarker Free 1 (pMF1) vector containing the green fluorescent protein (gfp) reporter gene to assess the effectiveness of steroid-inducible recombination and positive/negative dual selection to regenerate transgenic Cavendish banana plants that were potentially free of the selectable marker gene. By examining the interaction of two different Agrobacterium strains with two different cultivars of Cavendish banana, namely Williams and Grand Naine, we describe a transformation and regeneration strategy that successfully produced marker-free, single transgene copy, gfp-expressing events. The system will provide a useful means of serially improving banana into the future.

"It's Gonna be a Lifeline": Findings From Focus Group Research to Investigate What People Who Use Opioids Want From Peer-Based Postoverdose Interventions in the Emergency Department.

STUDY OBJECTIVE: Postoverdose interventions that deploy peer recovery support specialists to emergency departments (EDs) are a promising response to opioid overdoses among patients presenting in EDs. The objective of this study was to elicit patients' perspectives regarding the feasibility and acceptability of such an intervention and to ensure that their perspectives are represented in intervention design, implementation, and evaluation. METHOD: In 2019 the study investigators conducted focus groups with people who use opioids to elicit perspectives about a postoverdose intervention delivered in the ED by using a semistructured interview guide that asked about feasibility, acceptability, perceived benefits, and concerns. Focus groups were digitally recorded, transcribed, and analyzed for emerging themes. RESULTS: Nine focus groups with 30 people who use opioids were conducted. Key findings that could improve feasibility and acceptability of the intervention include the following: the importance of balancing the urgency of seeing patients quickly with a need to accommodate the experience of precipitated withdrawal symptoms; the need to address privacy concerns; and the need to address concerns related to cost, insurance coverage, and sustainability. Perceived benefits of the intervention included the ability of the peer recovery support specialist to provide advocacy and support, serve as a model of hope and encouragement for behavior change, and fill key service gaps. CONCLUSION: Postoverdose interventions in the ED provide the opportunity to integrate harm reduction-based interventions into traditional biomedical care facilities. These interventions can fill gaps in services and provide additional care and comfort for people who use opioids, but design, implementation, and evaluation should be informed by a patient-centered care perspective.

Molecular characterisation of a putative new polerovirus infecting pumpkin (Cucurbita pepo) in Kenya.

Next-generation sequencing of RNA extracted from a pumpkin plant with mosaic symptoms in Kenya identified the presence of a polerovirus sequence closely related to pepo aphid-borne yellows virus (PABYV). The near-complete polerovirus sequence comprised 5,810 nucleotides and contained seven putative open reading frames (ORFs) with a genome organisation typical of poleroviruses. BLASTp analysis of the translated sequences of ORFs 0, 1 and 2 revealed that their amino acid sequences differed by more than 10% from the corresponding protein sequences of other poleroviruses. These results suggest that this virus is a putative novel member of the genus Polerovirus, which has been provisionally named "pumpkin polerovirus" (PuPV).

Production of human vitronectin in Nicotiana benthamiana using the INPACT hyperexpression platform.

Human vitronectin (hVN) is a glycoprotein that functions as a cell adhesion molecule and a regulator of coagulation in blood plasma and the extracellular matrix. In vitro, hVN is added to serum-free media in order to promote the adhesion of animal cells to tissue culture surfaces and the proliferation of undifferentiated stem cells. Here, we report the production of hVN in Nicotiana benthamiana using the inducible In Plant ACTivation (INPACT) hyperexpression platform. N. benthamiana plants were transformed with an INPACT expression cassette encoding hVN, and both the Tobacco yellow dwarf virus Rep/RepA activator and Tomato bushy stunt virus p19 gene under the transcriptional control of the ethanol-inducible AlcR:alcA gene switch. hVN expression was maximal 4-5 days postactivation of the INPACT platform with a dilute ethanol solution, and crude yields of the recombinant protein reached a maximum of 643 ± 78 mg/kg fresh weight. A three-stage purification protocol was developed using heparin and polyhistidine tag affinity binding and size exclusion filtration, resulting in a plant-made hVN product of >90% purity. Storage conditions for plant-made hVN were identified that maximized the capacity of the recombinant protein to promote cell adhesion. Critically, plant-made hVN was shown to be functionally equivalent to commercial, plasma-derived hVN at promoting one-half maximal attachment of murine fibroblast cells (BALB-C/3T3) in serum-free medium at <0.1 µg/cm2 to tissue culture plasticware. The INPACT platform represents an attractive means of producing large quantities of functional, animal-free hVN for in vitro applications.

Characterization of an Australian isolate of taro bacilliform virus and development of an infectious clone.

The badnavirus taro bacilliform virus (TaBV) has been reported to infect taro (Colocasia esculenta L.) and other edible aroids in several South Pacific island countries, but there are no published reports from Australia. Using PCR and RCA, we identified and characterized an Australian TaBV isolate. A terminally redundant cloned copy of the TaBV genome was generated and shown to be infectious in taro following agro-inoculation. This is the first report of TaBV from Australia and also the first report of an infectious clone for this virus.

Golden bananas in the field: elevated fruit pro-vitamin A from the expression of a single banana transgene.

Vitamin A deficiency remains one of the world's major public health problems despite food fortification and supplements strategies. Biofortification of staple crops with enhanced levels of pro-vitamin A (PVA) offers a sustainable alternative strategy to both food fortification and supplementation. As a proof of concept, PVA-biofortified transgenic Cavendish bananas were generated and field trialed in Australia with the aim of achieving a target level of 20 µg/g of dry weight (dw) ß-carotene equivalent (ß-CE) in the fruit. Expression of a Fe'i banana-derived phytoene synthase 2a (MtPsy2a) gene resulted in the generation of lines with PVA levels exceeding the target level with one line reaching 55 µg/g dw ß-CE. Expression of the maize phytoene synthase 1 (ZmPsy1) gene, used to develop 'Golden Rice 2', also resulted in increased fruit PVA levels although many lines displayed undesirable phenotypes. Constitutive expression of either transgene with the maize polyubiquitin promoter increased PVA accumulation from the earliest stage of fruit development. In contrast, PVA accumulation was restricted to the late stages of fruit development when either the banana 1-aminocyclopropane-1-carboxylate oxidase or the expansin 1 promoters were used to drive the same transgenes. Wild-type plants with the longest fruit development time had also the highest fruit PVA concentrations. The results from this study suggest that early activation of the rate-limiting enzyme in the carotenoid biosynthetic pathway and extended fruit maturation time are essential factors to achieve optimal PVA concentrations in banana fruit.

Taxonomy of the order Mononegavirales: update 2017.

In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).

In plant activation: an inducible, hyperexpression platform for recombinant protein production in plants.

In this study, we describe a novel protein production platform that provides both activation and amplification of transgene expression in planta. The In Plant Activation (INPACT) system is based on the replication machinery of tobacco yellow dwarf mastrevirus (TYDV) and is essentially transient gene expression from a stably transformed plant, thus combining the advantages of both means of expression. The INPACT cassette is uniquely arranged such that the gene of interest is split and only reconstituted in the presence of the TYDV-encoded Rep/RepA proteins. Rep/RepA expression is placed under the control of the AlcA:AlcR gene switch, which is responsive to trace levels of ethanol. Transgenic tobacco (Nicotiana tabacum cv Samsun) plants containing an INPACT cassette encoding the ß-glucuronidase (GUS) reporter had negligible background expression but accumulated very high GUS levels (up to 10% total soluble protein) throughout the plant, within 3 d of a 1% ethanol application. The GUS reporter was replaced with a gene encoding a lethal ribonuclease, barnase, demonstrating that the INPACT system provides exquisite control of transgene expression and can be adapted to potentially toxic or inhibitory compounds. The INPACT gene expression platform is scalable, not host-limited, and has been used to express both a therapeutic and an industrial protein.

Complete genome sequence of a novel zantedeschia mild mosaic virus isolate: the first report from Australia and from Alocasia sp.

The complete genome of an Australian isolate of zantedeschia mild mosaic virus (ZaMMV) causing mosaic symptoms on Alocasia sp. (designated ZaMMV-AU) was cloned and sequenced. The genome comprises 9942 nucleotides (excluding the poly-A tail) and encodes a polyprotein of 3167 amino acids. The sequence is most closely related to a previously reported ZaMMV isolate from Taiwan (ZaMMV-TW), with 82 and 86 % identity at the nucleotide and amino acid level, respectively. Unlike the amino acid sequence of ZaMMV-TW, however, ZaMMV-AU does not contain a polyglutamine stretch at the N-terminus of the coat-protein-coding region upstream of the DAG motif. This is the first report of ZaMMV from Australia and from Alocasia sp.

Complete genome sequence of Colocasia bobone disease-associated virus, a putative cytorhabdovirus infecting taro.

We report the first genome sequence of a Colocasia bobone disease-associated virus (CBDaV) derived from bobone-affected taro [Colocasia esculenta L. Schott] from Solomon Islands. The negative-strand RNA genome is 12,193 nt long, with six major open reading frames (ORFs) with the arrangement 3'-N-P-P3-M-G-L-5'. Typical of all rhabdoviruses, the 3' leader and 5' trailer sequences show complementarity to each other. Phylogenetic analysis indicated that CBDaV is a member of the genus Cytorhabdovirus, supporting previous reports of virus particles within the cytoplasm of bobone-infected taro cells. The availability of the CBDaV genome sequence now makes it possible to assess the role of this virus in bobone, and possibly alomae disease of taro and confirm that this sequence is that of Colocasia bobone disease virus (CBDV).

Safety strategies and harm reduction for methamphetamine users in the era of fentanyl contamination: A qualitative analysis.

INTRODUCTION: In the United States, methamphetamine use is increasing and the context of its use has changed, with reports of illicitly manufactured fentanyl being mixed with methamphetamine (either deliberately or inadvertently). We explore risk-mitigating actions taken by people who use drugs to protect their health when using methamphetamine in that context. METHODS: We conducted qualitative interviews with 48 adults (18+) who used methamphetamine in the past three months at two sites in Nevada, USA and two sites in New Mexico, USA. Interviews were recorded, transcribed, and analyzed using thematic analysis. RESULTS: Respondents described two rationales for employing harm reduction strategies. First, to prevent harm from methamphetamine containing illicit fentanyl, and second, to maintain their general wellbeing while using methamphetamine. Regarding methamphetamine containing illicit fentanyl, our findings highlight how respondents employ primary strategies like buying from trusted sources and secondary strategies such as spotting and selective use of harm reduction tools (i.e., fentanyl test strips) to reduce risks. To maintain their general wellbeing, participants reduced their use of methamphetamine as reasonably as possible, and used other substances like marijuana and alcohol alongside methamphetamine to counter the unwanted side effects of methamphetamine (i.e., hallucinations and paranoia). Use of these harm reduction strategies varied within situational and social contexts, and respondents usually developed these strategies based on their lived experiences. CONCLUSION: Our findings uniquely demonstrate that people who use methamphetamine prioritize community driven, trust-based strategies within their social networks to mitigate risks in a fentanyl-contaminated drug environment. Additionally, our results indicate that harm reduction behaviors are influenced by multilevel risk environments, which include social, physical, economic, and political factors. Overall, these results highlight the potential for targeted interventions at the network level, which are responsive to complexities and shifts in drug market dynamics- such as illicit fentanyl in methamphetamine.

The effects of including sprouted barley with alfalfa hay in the diet on ruminal health and performance of cow-calf pairs.

The world population is growing exponentially, increasing demand to produce high-quality protein for human consumption. Changes in weather patterns, drought, and decreased land resources due to urbanization have increased the strain on the agriculture sector to meet world demands. An alternative method to combat these issues and continue to produce high-quality livestock feed would be through a controlled environment vertical farming system. Commonly, cereal grains, such as barley, are used in these systems to produce livestock feed. However, there is little information on the viability of feeding sprouted grains to beef cattle. Two diets of either feeder-quality alfalfa hay (n = 10 pairs; ALF) or the same alfalfa hay and sprouted barley (SB; 12.6% dry matter [DM]; n = 10 pairs) were fed for 90 d to Angus pairs with a steer calf during mid to late lactation. On days 0 and 90, body weight (BW), milk, rumen fluid, and body condition score were collected from cows and hip height and BW were recorded for calves. On day 10, BW was recorded for cows and calves and rumen fluid was collected from cows. Rumen fluid was also collected from cows on day 45. On day 55, BW was collected for both cows and calves and milk from cows. Intake was recorded throughout the trial via bunks with Vytelle technology. The PROC MIXED procedure of SAS was used to analyze all data with the day as a repeated measure to determine the main effect of diet. Individual volatile fatty acids (VFA) were measured as a percent of total VFA. No differences (P ≥ 0.16) were observed in calf BW, hip height, milk protein, fat, lactose, calf DM intake (DMI), or cow DMI. Cows fed SB tended (P = 0.08) to have a decreased somatic cell count compared to ALF. Percent butyrate was impacted by diet × day (P = 0.02), but no difference (P > 0.09) at any time points were detected. Additionally, a diet × day effect (P = 0.001) on rumen pH demonstrated that both groups stayed consistent until day 45 and then SB pH decreased the last 45 d. There was a day effect for total VFA (P = 0.0009), acetate:propionate (Ac:Pr; P < 0.0001), acetate (P < 0.0001), and propionate (P < 0.0001) demonstrating that total VFA, acetate, and Ac:Pr all increased throughout the trial, while propionate decreased. These results indicate that SB can be a potential alternative feed at this stage of production as it does not negatively impact health or production, but does affect the rumen pH and proportion of some VFA.

Climate variability and uncertainty associated with weather patterns can greatly impact feed security for cattle producers. Flooding, drought, and temperature extremes can reduce a farmer's ability to produce a consistent crop, resulting in feed prices that can fluctuate greatly. Vertical farming systems that sprout cereal grains in a controlled environment, using precision irrigation, may alleviate the effects of external factors such as climate and resulting feed prices. The objective of this study was to determine if sprouted barley (SB) could be used as an effective alternative feed source for cow-calf pairs. Two diets were fed to 20 cow-calf pairs, a control diet consisting of 100% feeder-quality alfalfa hay, or an experimental diet comprised of feeder-quality alfalfa hay and a 12.6% dry matter inclusion of SB for 90 d. Body weight, feed intake, and feeding behavior were analyzed in the cows and calves. Ruminal health was also assessed in cows by analyzing the ruminal fluid for pH and volatile fatty acid composition. When health and performance metrics were analyzed, no differences were found between the two diets that were administered to the cattle.

A qualitative study of interest in and preferences for potential medications to treat methamphetamine use disorder.

INTRODUCTION: We examined acceptability of and preferences for potential medications for treating methamphetamine use disorder (MUD) among people who use methamphetamine and examined how benefits and drawbacks of methamphetamine use affect perceived acceptability and preferences. METHODS: We conducted qualitative interviews as part of a larger study in 2019-2020. The interview assessed patterns of substance use (including methamphetamine), benefits and drawbacks of methamphetamine use, and interest in a medication to treat MUD. Analysis used an inductive thematic approach, guided by three primary questions: (1) would participants be interested in taking a potential medication for MUD?; (2) what effects would they would like from such a medication?; and (3) what would their ideal treatment route and schedule be (e.g. daily pill, monthly injection)?. RESULTS: We interviewed 20 people reporting methamphetamine use in the past 3 months (10 from Reno, Nevada, USA and 10 from Rio Arriba County, New Mexico, USA). Seven used exclusively methamphetamine, while thirteen used other substances in addition to methamphetamine. Most were enthusiastic about a potential medication to treat MUD. Of those who were not interested (n = 5), all indicated no current concerns about their methamphetamine use. Perceived functional benefits of methamphetamine use (i.e., energy, counteracting opioid sedation, and improved social and emotional wellbeing) informed preferences for a replacement-type medication that would confer the same benefits while mitigating drawbacks (e.g., psychosis, hallucinations, withdrawal). Opinions on preferred dosing varied, with some preferring longer acting medications for convenience, while others preferred daily dosing that would align with existing routines. CONCLUSION: Participants were excited about a potential for a medication to treat MUD. Their preferences were informed by the functional role of methamphetamine in their lives and a desire to maintain the stimulant effects while mitigating harms of illicit methamphetamine. Treatment outcomes that emphasize functioning and wellbeing, rather than abstinence, should be explored.

Patterns of and Rationale for the Co-use of Methamphetamine and Opioids: Findings From Qualitative Interviews in New Mexico and Nevada.

Introduction: Methamphetamine use and methamphetamine-involved deaths have increased dramatically since 2015, and opioid-related deaths now frequently involve methamphetamine. Nevada and New Mexico are states with elevated rates of opioid and methamphetamine use. In this paper, we report results from a qualitative analysis that examined patterns of methamphetamine and opioid co-use over participants' lifespan, factors that influence those patterns, and implications for health outcomes among users. Methods: Project AMPED was a multisite, mixed-methods study of methamphetamine use in Northern New Mexico and Northern Nevada. Between December 2019 and May 2020, qualitative interview participants were asked to describe their patterns of and reasons for co-administration of opioids and methamphetamine. Results: We interviewed 21 people who reported using methamphetamine in the past 3 months. Four primary patterns of methamphetamine and opioid co-use were identified: [1] using both methamphetamine and heroin, either simultaneously or sequentially (n = 12), [2] using methamphetamine along with methadone (n = 4), [3] using prescription opioids and methamphetamine (n = 1), and [4] using only methamphetamine (n = 4). Among those who used methamphetamine and heroin simultaneously or sequentially, motivations drew from a desire to enhance the effect of one drug or another, to feel the "up and down" of the "perfect ratio" of a goofball, or to mitigate unwanted effects of one or the other. Among those who used methamphetamine and methadone, motivations focused on alleviating the sedative effects of methadone. Conclusion: To address the emergent trend of increasing methamphetamine-related deaths, researchers, health care professionals, and community health workers must acknowledge the decision-making processes behind co-use of opioids and methamphetamine, including the perceived benefits and harms of co-use. There is an urgent need to address underlying issues associated with drug use-related harms, and to design interventions and models of treatment that holistically address participants' concerns.

Apoptosis-related genes confer resistance to Fusarium wilt in transgenic 'Lady Finger' bananas.

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most devastating diseases of banana (Musa spp.). Apart from resistant cultivars, there are no effective control measures for the disease. We investigated whether the transgenic expression of apoptosis-inhibition-related genes in banana could be used to confer disease resistance. Embryogenic cell suspensions of the banana cultivar, 'Lady Finger', were stably transformed with animal genes that negatively regulate apoptosis, namely Bcl-xL, Ced-9 and Bcl-2 3' UTR, and independently transformed plant lines were regenerated for testing. Following a 12-week exposure to Foc race 1 in small-plant glasshouse bioassays, seven transgenic lines (2 × Bcl-xL, 3 × Ced-9 and 2 × Bcl-2 3' UTR) showed significantly less internal and external disease symptoms than the wild-type susceptible 'Lady Finger' banana plants used as positive controls. Of these, one Bcl-2 3' UTR line showed resistance that was equivalent to that of wild-type Cavendish bananas that were included as resistant negative controls. Further, the resistance of this line continued for 23-week postinoculation at which time the experiment was terminated. Using TUNEL assays, Foc race 1 was shown to induce apoptosis-like features in the roots of wild-type 'Lady Finger' plants consistent with a necrotrophic phase in the life cycle of this pathogen. This was further supported by the observed reduction in these effects in the roots of the resistant Bcl-2 3' UTR-transgenic line. This is the first report on the generation of transgenic banana plants with resistance to Fusarium wilt.

Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.).

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.