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BackgroundThe genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses.ResultsTo help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format.ConclusionsThe VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/ . We welcome participation from the community in developing the file format standard, as well as code contributions.

Engineered nanomaterials (ENMs) are increasingly entering the environment with uncertain consequences including potential ecological effects. Various research communities view differently whether ecotoxicological testing of ENMs should be conducted using environmentally relevant concentrations-where observing outcomes is difficult-versus higher ENM doses, where responses are observable. What exposure conditions are typically used in assessing ENM hazards to populations? What conditions are used to test ecosystem-scale hazards? What is known regarding actual ENMs in the environment, via measurements or modeling simulations? How should exposure conditions, ENM transformation, dose, and body burden be used in interpreting biological and computational findings for assessing risks? These questions were addressed in the context of this critical review. As a result, three main recommendations emerged. First, researchers should improve ecotoxicology of ENMs by choosing test end points, duration, and study conditions-including ENM test concentrations-that align with realistic exposure scenarios. Second, testing should proceed via tiers with iterative feedback that informs experiments at other levels of biological organization. Finally, environmental realism in ENM hazard assessments should involve greater coordination among ENM quantitative analysts, exposure modelers, and ecotoxicologists, across government, industry, and academia.

BackgroundWe have previously demonstrated that cerebrospinal fluid-derived B cells from early relapsing-remitting multiple sclerosis (RRMS) patients that express a VH4 gene accumulate specific replacement mutations. These mutations can be quantified as a score that identifies such patients as having or likely to convert to RRMS. Furthermore, we showed that next generation sequencing is an efficient method for obtaining the sequencing information required by this mutation scoring tool, originally developed using the less clinically viable single-cell Sanger sequencing.ObjectiveTo determine the accuracy of MSPrecise, the diagnostic test that identifies the presence of the RRMS-enriched mutation pattern from patient cerebrospinal fluid B cells.MethodsCerebrospinal fluid cell pellets were obtained from RRMS and other neurological disease (OND) patient cohorts. VH4 gene segments were amplified, sequenced by next generation sequencing and analyzed for mutation score.ResultsThe diagnostic test showed a sensitivity of 75% on the RRMS cohort and a specificity of 88% on the OND cohort. The accuracy of the test in identifying RRMS patients or patients that will develop RRMS is 84%.ConclusionMSPrecise exhibits good performance in identifying patients with RRMS irrespective of time with RRMS.

This article discusses the measurement and interpretation of vitellogenin (VTG) in fish and amphibians as a biomarker for endocrine activity. The reliability and acceptability of VTG results are important for regulatory assessments of chemicals. The article highlights the variability in VTG measurements and the need for improvement in sampling, quantification, and data handling. It proposes a decision logic to assist in the interpretation of VTG measurements and calls for the development of OECD guidance on best practices for VTG assessment. The article emphasizes the importance of considering other factors and endpoints in conjunction with VTG results to determine endocrine activity. [Extracted from the article]

Breakdown products of the wood structural polymer lignin are major components in the effluent from commercial pulp and paper manufacturing mills. Polar lignin-derived macromolecules (LDMs) isolated from vastly different pulping processes and from different source wood have surprisingly similar properties and biological activity. Our group has previously reported that a LDM from bleached Kraft mill effluent (BKME) inhibits sea urchin fertilization by binding to sperm cells and blocking the egg jelly induced acrosome reaction. Lignosulfonic acid (LSA), an LDM from sulfite mill effluent, is structurally distinct from BKME-LDM and data presented herein indicate that it was a more potent inhibitor of fertilization. LSA ranged in molecular size from 300K, with higher molecular size fractions being the more potent inhibitors of fertilization. The mode of action of LSA on sea urchin fertilization was characterized by examining its effects on two critical prerequisite sperm-egg interactions: acrosome reaction induction by egg jelly and sperm-to-egg binding. LSA inhibited both of these processes at low concentrations. Microscopically, a biotinylated LSA derivative (LSA-b) bound to localized domains of the sperm surface, particularly over the head and acrosomal regions. The interaction of LSA with binding sites on the sperm surface was further characterized using a quantitative solid phase whole-cell binding assay and the LSA-b probe. LSA-b behaved in a manner consistent with receptor-ligand binding models in that its interaction with sperm was specific, saturable, kinetically dependent, and reversible. LSA specifically inhibited the binding of antibodies to proteins that entirely co-localize within its binding domain, sea urchin receptor for egg jelly (suREJ3) and bindin. These results support the hypothesis that LSA exerts its biological action by binding to key molecules involved in gamete recognition.