The complete genome sequence of Piper yellow mottle virus (PYMoV)

This study reports the first complete genome sequence of Piper yellow mottle virus (PYMoV, KC808712) identified in black pepper. The genome is 7,622 nucleotides long, possessing four open reading frames (ORFs). ORF1, ORF2 and ORF4 of PYMoV are reported as hypothetical proteins of unknown function with a predicted molecular mass of 15.7, 17.1 and 17.9 kDa, respectively. ORF3 of PYMoV encodes a polyprotein of 218.6 kDa and consists of a viral movement protein (MP), trimeric dUTPase, zinc finger, retropepsin, RT-LTR, and RNAse H. Detailed PYMoV genome analysis confirmed that it is a member of the family Caulimoviridae, genus Badnavirus. Fragments of two additional novel sequences resembling those found in members of the family Caulimoviridae were also identified in the black pepper sample, and the viruses from which they were derived were tentatively named Piper DNA virus 1 and 2.

Interaction of the N-methyl-D-aspartic acid receptor NR2D subunit with the c-Abl tyrosine kinase

The COOH-terminal domain of the NR2D subunit of the NMDA receptor contains proline-rich regions that show striking homology to sequences known to bind to Src homology 3 (SH3) domains. To determine whether the proline-rich region of the NR2D subunit interacts with specific SH3 domains, in vitro SH3 domain binding assays were performed. A proline-rich fragment of the NR2D subunit (2D(866-1064)) bound to the Abl SH3 domain but not to the SH3 domains from Src, Fyn, Grb2, GAP, or phospholipase C-gamma (PLCgamma). Co-immunoprecipitation of NR2D with Abl suggests stable association of NR2D and Abl in transfected cells. The SH3 domain plays an important role in the negative regulation of Abl kinase activity. To determine whether the interaction of NR2D with the Abl SH3 domain alters Abl kinase activity, Abl was expressed alone or with NR2D in 293T cells. Autophosphorylation of Abl was readily observed when Abl was expressed alone. However, co-expression of Abl with 2D(866-1064) or full-length NR2D inhibited autophosphorylation. 2D(866-1064) did not inhibit DeltaSH3 Abl, indicating a requirement for the Abl SH3 domain in the inhibitory effect. Similarly, 2D(866-1064) did not inhibit the catalytic activity of Abl-PP, which contains two point mutations in the SH2-kinase linker domain that release the negative kinase regulation by the SH3 domain. In contrast, the full-length NR2D subunit partially inhibited the autokinase activity of both DeltaSH3 Abl and Abl-PP, suggesting that NR2D and Abl may interact at multiple sites. Taken together, the data in this report provide the first evidence for a novel inhibitory interaction between the NR2D subunit of the NMDA receptor and the Abl tyrosine kinase.

The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses

The complete nucleotide sequences of RNA 1 and RNA 2 of the nepovirus potato black ringspot virus (PBRSV) from two different isolates were determined, as well as partial sequences from two additional isolates. RNA1 is 7,579-7,598 nucleotides long and contains one single open reading frame (ORF), which is translated into a large polyprotein with 2,325 amino acids and a molecular weight of 257 kDa. The complete sequence of RNA2 ranges from 3857 to 3918 nt between the different isolates. It encodes a polyprotein of 1079-1082 amino acids with a molecular weight of 120 kDa. Sequence comparison using the Pro-Pol region and CP showed that all four isolates formed two distinct groups, corresponding to potato and arracacha, that were closely related to each other and also to tobacco ringspot virus (TRSV). Comparing our data to those obtained with other nepoviruses, our results confirm that PBRSV belongs to a distinct species and is a member of subgroup A in the genus Nepovirus based on its RNA2 size, genome organization, and nucleotide sequence.

Genomics informed design of a suite of real-time PCR assays for the specific detection of each Xylella fastidiosa subspecies

AIMS

Existing methods for the identification of the subspecies of Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and the associated plant health response to outbreaks and interceptions.

METHODS AND RESULTS

Diagnostic markers were identified using a comparative genomics approach to allow fine differentiation of the very closely related subspecies. Five qPCR assays were designed to allow specific detection of X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, X. fastidiosa subsp. pauca, X. fastidiosa subsp. morus and X. fastidiosa subsp. sandyi. All assays were validated according to the European and Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2).

CONCLUSIONS

All of the assays were shown to be specific to the target subspecies and all the assays could be used to detect femtogram quantities of X. fastidiosa DNA.

SIGNIFICANCE AND IMPACT OF THE STUDY

At present, diagnosing the subspecies of X. fastidiosa requires multiple conventional PCR assays (although only available for three of the five subspecies) or multi-locus sequence typing which takes several days. By comparison, the new assays provide a substantial reduction in the turnaround time for direct identification to the subspecies level in as little as 75 min.

Opportunities for recycling in an automated clinical chemistry laboratory produced by the comprehensive metabolic panel

OBJECTIVES

Clinical laboratories perform a variety of tests for which biomedical waste is a byproduct. Of these, the complete metabolic panel (CMP) produces a significant portion of this waste. We investigated specific waste subsequent to performing CMPs over the course of a year and analyzed what percentage of the waste produced could have been recycled.

METHODS

Patient testing volumes were collected retrospectively from July 14, 2021, to July 14, 2022, for individual assays within the CMP performed on Abbott Alinity c instruments (n = 6). The average weights for components of the reagent kits, which includes wedges, boxes, and package inserts, were calculated. These weights, in conjunction with total patient testing volumes, were used to determine the amount of waste produced.

RESULTS

A total of 1089.2 kg of reagent kit waste was estimated to be produced by performing CMPs throughout a year. Of this waste, most (855.5 kg) was not recyclable, but a subset (233.6 kg) was. Overall, 21.4% of the total specific waste weight was found to be recyclable.

CONCLUSIONS

The CMP contributes a substantial amount of waste when performed on chemistry analyzer platforms in the clinical laboratory. Paper inserts and cardboard packaging, however, presented opportunities for recycling.

The engorgement enigma

A search of the literature reveals only a few studies that deal directly with engorgement. When the relevant research is analysed, a picture emerges of the causes of engorgement, how it can be prevented and what is the best management when it occurs. Equipped with this information, people providing support to breastfeeding mothers can encourage preventative behaviours, and assess and educate mothers at risk, thus allowing the majority of mothers and babies to breastfeed naturally without intervention.

Can state mental health agencies survive health care reform?

State mental health systems have undergone dramatic changes in the last 40 years, including decreases in state hospital capacity and increases in the proportion of mental health care provided in ambulatory settings and in general hospital units and private psychiatric hospitals. Health care reform is likely to accelerate these changes. The authors consider whether state mental health agencies have a future, given that they were created to operate state hospitals, a role that has been greatly diminished. The authors suggest that state mental health agencies will continue to exist, but that their role will change significantly.

Meeting the governance challenges of integrated health and social care

Background

Many countries are experimenting with novel ways of organising and delivering more integrated health and social care. Governance is relatively neglected as a focus of attention in this context but addressing governance challenges is key for successful collaboration.

Methods

Cross-country case analysis involving document review and semi-structured interviews with 27 local, regional and national level stakeholders in Italy, the Netherlands and Scotland. We used the Transparency, Accountability, Participation, Integrity and Capability (TAPIC) framework to structure our analytical enquiry to explore factors that influence the governance arrangements in each system.

Results

Governance arrangements ranged from informal agreements in the Netherlands to mandated integration in Scotland. Novel service models were generally participative involving a wide range of stakeholders, including the public, although integration was seen to be driven, largely, from a health perspective. In Italy and Scotland some reversion to ‘command & control’ was reported in response to the imperatives of the Covid-19 pandemic. Policies, budgets, auditing and reporting systems that are clearly aligned at all levels were seen to help with implementing innovations in service organisation. Where alignment was lacking, cooperation and integration was suboptimal, regardless of whether governance arrangements were statutory or not. There was wide recognition of the importance of buy-in. Enablers of greater engagement included visible leadership, time and long-standing working relationships. Lack of suitable indicators and openness to data sharing to measure integration hindered working relationships and thus the successful delivery of integrated services.

Conclusions

Our study provides important insights into how to more effectively and efficiently govern service delivery structures within care systems. We will discuss approaches to governance that help support more resilient integrated care systems.

Key messages

• Different governance arrangements face common challenges to greater integration of care. Enablers include strong leadership, inclusivity and openness to work across traditional boundaries.

• Meeting the governance challenges of integrated health and social care requires clear lines of accountability, aligned policies, budgets and reporting systems.