The UK Cellular Microbiology Network held its inaugural conference in February 2019. This stimulating day of scientific exchange will be the first of many, its organisers hope. These allow better opportunities for personal connections, but also permit focusing on topics that seldom get much airplay in modern, multi‐stream mega‐symposia. They can also serve to create and consolidate valuable regional or national networks.The cellular microbiology of bacterial pathogens is one such niche topic within the greater umbrella of microbiology, with its exotic array of viral, fungal, and bacterial microbes jockeying for position, alongside the competing interests of the immunological response. In an era of increasing antibiotic resistance, furthering our understanding of how prokaryotes interact with their host cells, and developing novel ways to intervene, has never been more important. Despite this imperative, conferences focusing on this topic are rare, and its researchers are often situated in academic departments with different foci, meaning that they can sometimes feel like isolated members of a diaspora and often struggle to meet valuable collaborators.For this reason, we decided to organise an annual forum in the United Kingdom—dubbed “The UK Cellular Microbiology Network”—devoted to the cell biology of host‐bacterial interactions. Despite the national emphasis, we were keen to welcome any of our geographical neighbours who wished to attend. We wanted to focus specifically on how bacterial pathogens subvert host cellular processes and how the host cell responds. In creating an engaging, affordable, and informal meeting showcasing the work of early‐career researchers, we hoped to encourage the forging of useful collaborations and cross‐fertilisation of diverse expertise and experiences about host cell biology across the wide variety of bacterial pathogens under study.Journal of Cell Science, Perkin Elmer, Zeiss—and this journal, Cellular Microbiology. In addition to the programme of talks, we also had a vibrant poster session and ended the evening with drinks, nibbles, and serious networking in the Crick's lovely gallery space.Our inaugural one‐day meeting was held at London's Francis Crick Institute on 11 February 2019 .The meeting kicked off with the first of our two keynote speakers, Carmen Buchrieser from the Institut Pasteur in Paris. Challenging her audience with the idea that Salmonella Typhi, Angela Ibler (from Dan Humphreys' lab at the University of Sheffield) demonstrated beautifully how secreted bacterial factors can have an impact on host cell states. Using stunning super‐resolution microscopy images, she showed that the toxin can induce a novel nuclear DNA damage response, called the Response Induced by the bacterial Genotoxin (RING), which was caused by replicative stress resulting from reduced cellular levels of a single‐stranded DNA‐binding protein. Interestingly, this new RING pathway also triggered a transmissible senescence‐like state in cells, which in turn made cells more susceptible to S. Typhi infection. This research suggests a new virulence mechanism that may be relevant to chronic Salmonella infections. And Angela's talk was so accomplished that she won the prize for best oral presentation—a pair of snazzy binoculars courtesy of Zeiss for whenever she fancies taking a break from the microscope .Secretion—a popular virulence strategy amongst prokaryotes—featured in two additional talks. Focusing on the typhoid toxin produced by the human pathogen Staphylococcus aureus. Watkins demonstrated with striking timelapse videomicroscopy images that S. aureus mutants lacking different components of the T7SS were deficient in their ability to escape from macrophages. She showed that T7SS modulated the type of cell death triggered in macrophages, indicating a key role of this system in S. aureus‐macrophage interactions.Carrying on with the theme that bacterial pathogens employ a number of secretion systems critical for intracellular bacterial survival, Kate Watkins (from Meera Unnikrishnan's group at the University of Warwick) presented her studies on the intriguing type VII bacterial secretion system (T7SS) of the Gram positive pathogen, Mycobacterium tuberculosis highlighted this theme. Susanne Herbst (Max Gutierrez's lab at the Francis Crick Institute) showed that a kinase commonly associated with Parkinson's disease, LRRK2, has an immune function in macrophages. She showed that cultured primary mouse and human macrophages lacking LRRK2 were able to better control M. tuberculosis infection. On the basis of the data she presented, it is tempting to hypothesise that infectious diseases and macrophage responses could play an important role in the pathogenesis of Parkinson's disease. This finding adds to the growing evidence that the immune response contributes to neurodegeneration, which may open the door to innovative new therapies.Of course, macrophages are a popular host cell for a wide variety of pathogens seeking to gain easy cellular entry and the upper hand against the immune response. Their subversion formed another thread at the meeting, and two talks about the obligate intracellular bacteria M. tuberculosis infection. Interestingly, he showed that IRG‐1 is recruited to M. tuberculosis‐containing phagosomes and that this enzyme is required for the control of bacterial replication in macrophages. Immunometabolism is a field of growing interest, and knowing more about the role of such metabolites in infection may lead to novel alternatives to antibiotics.It is known that immune cell metabolism is key for the establishment of an appropriate immune response. Eik Hoffmann  showed that mice lacking the enzyme IRG‐1, which regulates the production of the metabolite Itaconate, are not able to control Streptococcus pneumoniae, sequestered within splenic macrophages, can lead to sepsis after initial clearance in mice. Joe Wanford from this group wanted to see whether this was the case in humans. He reported an innovative organ‐slice perfusion model derived from experimentally infected ex vivo human spleens from patients undergoing elective splenectomy, which showed that intracellular bacteria accumulate with time post‐clearance, after a single monoclonal founder replicates to form a cluster. These data have obvious implications for how invasive pneumococcal disease should be treated.Carrying on with the hijacked macrophage theme, the group of Marco Oggioni (University of Leicester) previously published that a single founder bacterium of Salmonella in vivo. Unexpectedly, he discovered that NRAMP1‐mediated resistance against infection is mediated by magnesium starvation, suggesting new strategies for infection control.Host cells are not always as vulnerable as they look, and cellular mechanisms that recognise and eliminate invasive bacterial pathogens are the subject of intense investigation. NRAMP1  is a divalent‐metal efflux pump at the phagosomal membrane in macrophages, and mutations in NRAMP1 cause susceptibility to several intracellular pathogens. Using cutting edge single‐cell techniques, Olivier Cunrath  is looking to identify the precise mechanism of NRAMP1‐mediated resistance against , MRC Laboratory for Molecular Biology) discovered that members of the interferon‐induced GTPase family of guanylate‐binding proteins (GBPs) control Gram‐negative bacteria that can invade the cytosol . GBPs form a noncanonical inflammasome on the pathogen surface to initiate pyroptotic cell death of infected cells by recruiting and activating the cytosolic lipopolysaccharide receptor, Caspase‐4. Strikingly, Shigella can counteract GBP‐mediated cell‐autonomous immunity to inhibit cell death and form actin tails important for bacterial dissemination. As the next step, it will be of great interest to investigate the precise function for GBPs in host defence against cytosolic pathogens.Previous work has shown that interferon exposure promotes cell‐autonomous immunity for pathogen control, but the underlying mechanisms are poorly understood. Michal Wandel  showed us a holistic view of how proteins on phagosomes of activated macrophages are ubiquitinated. He demonstrated how immune activation qualitatively changes the phagosomal ubiquitin‐linkage landscape, identifying a plethora of novel targets that can potentially be modulated to target phagosomal pathogens. In fact, some of these ubiquitin‐modulating targets that regulate phagosome biology might be one day exploited as host‐directed therapies.Salmonella typhimurium effector proteins specifically target the small GTPase Rab32 to promote intracellular survival. She also presented new unpublished evidence of the importance of the Rab32/BLOC3 pathway in controlling Salmonella Typhi infection.But the bacteria always seem to be one step ahead. Virtu Solano Collado (from Stefania Spano's lab at the University of Aberdeen) shared the latest update on her work investigating how Salmonella is able to subvert host trafficking pathways. Virtu described how https://hrman.org/). Using a variety of intracellular pathogens including the cellular microbiology paradigm S. Typhimurium, he showcased HRMAn's capacity to recognise and quantify various attributes of host‐pathogen interactions. In this way, HRMAn can inspire a broad range of cellular microbiologists to perform high‐content image analysis.The field of cellular microbiology is exploding in part due to exciting advances in high resolution and high‐content microscopy. To quantify image‐based host‐pathogen interactions in an unbiased manner, Daniel Fisch (from Eva‐Maria Frickel's lab at the Francis Crick Institute) employed an artificial intelligence workflow to develop an image analysis platform called HRMAn  was Thierry Soldati from the University of Geneva. Soldati—this journal's Editor‐in‐Chief—has pioneered the use of the amoeba Dictyostelium discoideum as a surrogate host for mycobacterial infections. In his keynote speech, he summarised some of his team's discoveries about how Mycobacterium marinum subvert and escape the phagosome, as well as spread between cells. He also described their most recent work showing, intriguingly, how Dictyostelium cells are able to exclude their infected brethren when they undergo multicellular development, effectively clearing the infection from the population.The final speaker of the day (kindly sponsored by In conclusion, the first meeting of the new Network was highly successful, exciting, and left everyone with much food for thought, along with new connections. And we liked it so much that we are doing it all over again in February 2020—this time in Sheffield. Please do join us!


Germ cell tumours are uniquely associated with the gametogenic tissues of males and females. A feature of these cancers is that they can express genes that are normally tightly restricted to meiotic cells. This aberrant gene expression has been used as an indicator that these cancer cells are attempting a programmed germ line event, meiotic entry. However, work in non‐germ cell cancers has also indicated that meiotic genes can become aberrantly activated in a wide range of cancer types and indeed provide functions that serve as oncogenic drivers. Here, we review the activation of meiotic factors in cancers and explore commonalities between meiotic gene activation in germ cell and non‐germ cell cancers.The objectives of this review are to highlight key questions relating to meiotic gene activation in germ cell tumours and to offer possible interpretations as to the biological relevance in this unique cancer type.GEPIA database were searched for papers in English and for cancer gene expression data, respectively.PubMed and the We provide a brief overview of meiotic progression, with a focus on the unique mechanisms of reductional chromosome segregation in meiosis I. We then offer detailed insight into the role of meiotic chromosome regulators in non‐germ cell cancers and extend this to provide an overview of how this might relate to germ cell tumours.We propose that meiotic gene activation in germ cell tumours might not indicate an unscheduled attempt to enter a full meiotic programme. Rather, it might simply reflect either aberrant activation of a subset of meiotic genes, with little or no biological relevance, or aberrant activation of a subset of meiotic genes as positive tumour evolutionary/oncogenic drivers. These postulates provide the provocation for further studies in this emerging field. Given this, much of what is known about the regulation of meiotic initiation and the mechanisms of meiotic chromosomes segregation comes from studies in model eukaryotes, particularly murine systems, with a greater emphasis on spermatogenesis  at the developing gonad, the cells undergo extensive epigenetic reprogramming, and development is directed either towards ovaries or testis depending on the presence or absence of a functioning Witchel, . There aWitchel, . HoweverWitchel,   gene expression  coupled with et al., During pre‐meiotic DNA replication, newly formed sister chromatids remain connected via the actions of a ring structure termed cohesin that encircles both sister chromatids ‐MND1 Hunter,  Figs 1B mbt gene are shifted to the non‐permissive condition mbt tumour formation were mei‐W68 and mei‐P22, the orthologues of human SPO11 and TOPOVIBL, respectively  for tumour formation could be suppressed, to some degree, by ionizing irradiation, suggesting that the function that Mei‐W68 mediates is DSB‐associated   genes are a class of gene that has expression normally restricted to the testis of adult males, but which become active in some, if not even all cancers .However, new evidence has recently emerged to suggest a link between meiotic recombination hot spots and genome stability mbt tumour studies do not shed any light on whether TEX19 is required early in the oncogenic programme, as well as being required to maintain the proliferative status of cancer cells, although preliminary analysis of human tumour progression arrays suggests that it is activated early in the oncogenic programme , which interconnects homologous chromosomes . SCYP3 produced outside the meiotic context has been shown to disrupt the activity of the tumour‐suppressing recombination regulator BRCA2 and can modulate the strand invasion capabilities of both the RAD51 and DMC1 (meiosis‐specific) recombinases that drive homologous recombination  and oxidative stress resistance in lung adenocarcinomas . It is proposed that HORMAD1 mediates rucaparib resistance by activating a distinct DSB repair pathway that suppresses the synthetic lethality of rucaparib and failed DSB repair. Indeed, Watkins et al.  and serves to irrefutably demonstrate the potential for imposition of meiotic cohesin function in mitotic cells by aberrant expression of only a single meiotic cohesin gene. In humans, this picture is less clear as expression of the human REC8 gene does not appear to be restricted to the testes  and into those that are not   are currently classified into tumours that are derived from germ cell neoplasia et al., et al., et al., et al., et al., et al., et al., Whilst the cells of origin for the various tumour types have somewhat been pinpointed, it is not clear how these tumour cells maintain a proliferative programme. In a normal developmental setting, PGCs at extragonadal sites as well as at the developing ovaries enter meiosis  and GTEx ? I think this is an interesting and open question and we should keep an open mind and look to generate data to support or refute all options.In the NTERA‐2 cell line with TEX19 knock down, did you exclude that you were not only stopping proliferation, but perhaps you were simply seeing cell differentiation?OCT4 expression following TEX19 knockdown to address whether reduction in TEX19 levels triggered differentiation; we could find no overt evidence that differentiation was occurring. We used both HMBA and RA treated NTERA‐2 cells as controls. We also assessed what happens to TEX19 expression following differentiation induced by either RA or HMBA and found that whilst OCT4 RNA levels were reduced quite quickly, TEX19 transcript levels stayed relatively high until complete differentiation, suggesting there is not an obvious correlation to OCT4.The NTERA‐2 cell line is capable of undergoing differentiation. Treatment with retinoic acid (RA) causes differentiation along a neuronal lineage whereas HMBA treatment results in differentiation down ill‐defined lineages. We assessed cell morphology changes and BRCA2 gene, but have you looked at other DNA repair genes such as TP53, which possibly explains the sensitivity of seminoma to treatment?You mentioned the YCP3 does become expressed in germ line tumours, so disruption of BRCA2 activity in germ line tumours by meiotic factors is an interesting possibility.We have not studied BRCA2 directly in our experiments although others have demonstrated that the meiosis‐specific SYCP3 protein can disrupt BRCA2 function. Whilst I'm not aware that this has been studied extensively in germ line tumours, SNo we have not explored a relationship between other meiotic factors and TP53 in germ line tumours.In meiosis, there is a reduction of chromosomes from 2N to 1N, whereas, in testicular tumours there is duplication of chromosomes from 2N to 4N. Can you speculate what is driving this change?This is possible premeiotic replication without subsequent segregation. Alternatively, there are other pathways that could cause ploidy changes due to meiotic gene activation, not least of which is the aberrant formation of mono polar centromeric associations between sister centromeres by the activation of REC8 cohesin function – this would explain the centromeric homozygocity observed in some germ line tumours.


Cryptolaemus montrouzieri, we used a reduced‐representation sequencing method to analyze the genome‐wide differentiation of the samples from two native and five introduced locations. Our analyses based on a total of 53,032 single nucleotide polymorphism loci showed that beetles from the introduced locations in Asia and Europe exhibited significant reductions in genetic diversity and high differentiation compared with the samples from the native Australian range. Each introduced population belonged to a unique genetic cluster, while the beetles from two native locations were much more similar. These genomic patterns were also detected when the dataset was pruned for genomic outlier loci , suggesting that random genetic drift was the main force shaping the genetic diversity and population structure of this biological control agent. Our results provide a genome‐wide characterization of polymorphisms in a biological control agent and reveal genomic differences that were influenced by the introduction history. These differences might complicate assessments of the efficiency of biological control and the invasion potential of this species but also indicate the feasibility of selective breeding.Biological control is the main purpose of intentionally introducing non‐native invertebrate species. The evolutionary changes that occur in the populations of the introduced biological control agents may determine the agent's efficiency and the environmental safety. Here, to explore the pattern and extent of potential genomic changes in the worldwide introduced predatory ladybird beetle The intentional introduction of invertebrate species is generally used as a form of biological control , is native to Australia and is a predator specialist of mealybug  markers, we found high and significant genetic differentiation between native and introduced populations  and bioinformatic tools have spurred the development of genome‐wide genetic markers for studying the ecology and evolution of nonmodel organisms , dNTPs, and adapter primers. The PCR products were purified using Agencourt AMPure XP  and subjected to electrophoresis through a 2% agarose gel. Fragments in the size range of 250–350 bp were excised and purified using a QIAquick Gel Extraction Kit . The samples with indexes were allocated to a single lane and subjected to 150 bp paired‐end sequencing on the HiSeq 2500 platform  at Biomarker Technologies Corporation (China). Real‐time monitoring was performed for each cycle during sequencing. The ratio of high‐quality reads exhibiting Q30  and the guanine‐cytosine (GC) content of the raw reads were calculated for quality control.Approximately 500 ng of genomic DNA from each sample was processed for reduced‐representation genome sequencing using the specific‐locus amplified fragment sequencing (SLAF‐seq) technique  higher than 0.75  for each SNP were calculated using PLINK, and those loci that significantly deviated from HWE at more than three studied locations were excluded. The filtered SNPs were mapped to the annotated transcriptome of the species  iterations. The q‐values for each locus in AH and ANH were subsequently calculated from the p‐value with p.adjust in R to monitor the false discovery rates (FDRs). Those loci with q‐values below 0.05 were considered FST outliers. Some simulation studies have suggested that potential error rates must be evaluated by interpreting the results with a variety of methods . Genetic diversity and population structure were analyzed based on the total loci, the neutral loci, and the high FST outlier loci.To detect the contribution of different loci to the diversity of this biological control agent, the total SNPs were further separated into three datasets, which included the high and low HO), and expected heterozygosity (HE). Comparisons of these parameters between native and introduced locations were performed using t tests in SPSS 21 .We employed Arlequin to calculate genetic diversity parameters at each of the studied locations, including the percentage of polymorphic loci (Poly%), nucleotide diversity (Pi), observed  the reconstruction of phylogenetic trees, (b) the estimation of ancestry proportions, and (c) an analysis of molecular variation (AMOVA). Neighbor‐joining (NJ) trees were reconstructed in MEGA6 . We explained the genetic structure by obtaining the lowest cross‐validation error from K = 2 to 10. Then, AMOVA was performed in Arlequin with 10,000 permutations to further test for the population structure identified by clustering with ADMIXTURE.We calculated overall and pairwise 33.1A total of 504.25 million reads were obtained from the raw sequencing data. The sequencing quality of each sample is shown in Supporting Information Table HO, a single SNP per tag, and HWE , MAF, WE Table .3.2FST outliers , acetyl‐CoA acyltransferase , glycine‐tRNA ligase , and the calcium‐activated potassium channel slowpoke .The allele frequencies of the high s Figure a. A totae Figure b, some o3.3FST outlier loci). The results based on the datasets containing all loci and the neutral loci only were similar, while the results based on the high FST outlier loci were quite different. Significant reductions in the number of polymorphic loci and nucleotide diversity were found when the introduced populations were compared to the native populations . There was no significant difference in HO and HE values between the native and introduced locations.The genetic diversity parameters of each studied location are shown in Table C. montrouzieri samples was very similar between the dataset with all loci and only the neutral loci. In the dataset with all loci, we detected high differentiation among global populations . The pairwise FST values among the studied locations are shown in Table FST = 0.017, p < 0.001), while all introduced populations showed much higher differentiation compared to the native populations . All of the introduced populations were also highly differentiated from each other . The NJ tree clustered individuals largely by population of origin, placing individuals from the native Australian range  in the middle of separate branches leading to the introduced populations SA, GT, and TP as well as the common branch to SY and SZ  was higher and significant for K = 6 structuring . Our genome‐wide description of polymorphisms in the ladybird C. montrouzieri demonstrates ample genetic variation and thus suggests that such approaches might be promising avenues for further improvements of the performance of this biological control agent.Second, the extent of the detected genetic changes might indicate the feasibility of selective breeding for improvement of traits of interest .All raw sequences are available in the NCBI SRA databases . The filtered 53,032 SNPs used in this study are available at Dryad ( Click here for additional data file. Click here for additional data file.


The therapeutic options for patients with CLL have developed remarkably within recent years, as several new drugs have paved the way to a chemotherapy–free treatment paradigm. A general feature of these drugs is their ability to induce cell death in a p53–independent manner, however their use is not restricted to CLL with defects in the TP53 pathway. The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has proven to be highly effective in both first–line and relapse. Results from the ILLUMINATE, Alliance North American Intergroup Study A041202 and ECOG–ACRIN E1912 trials show superiority of ibrutinib over varoius chemoimmunotherapy standard regimens in previously untreated CLL [The orally available BCL–2 inhibitor venetoclaxcan induce apoptosis in a p53–independent manner, by displacing pro–apoptotic proteins like BIM and BAX from binding to BCL–2 and therefore inducing apoptosis. In CLL, which is universally characterized by high abundance of BCL–2, venetoclax seems to be the most effective single agent. Already the initial Phase 1 study showed substantial response rates and a manageable toxicity after adjustment to a dose escalation schedule . The M13However, despite this high effectivity, patients candevelop secondary resistance to venetoclax over time with continuous drug administration. In the M13–982 trial the estimated duration of response at 24 months decreased to66% . SpecifiIn order to minimize the risk for acquisition ofsecondary resistance, combination therapies and time limited treatment have been investigated. Based on the results of the phase III MURANO trial, the combination of venetoclax with rituximab has been licensed by FDA and EMA in patients with relapsed I refractory CLL irrespective of dell7p. In this trial venetoclax was given for a limited period of 2 years in combination with 6 administrations of Rituximab and compared to 6 cycles rituximab and bendamustine. The 24 months progression free survival estimates were 84.9% versus 36.3%, respectively, indicating that time limited combination therapies are also highly effective [Current efforts in clinical trials are aiming to combine venetoclax with other highly effective novel drugs like obinutuzumab and ibrutinib in a time limited setting. In the CAPTIVATE trial the combination of ibrutinib and venetoclax in first–line therapy already achieved CR rates of 100% and MRD negativity in 82% . The comDue to the high rate of deep responses and long remission durations combined with good tolerability, venetoclax–based combination treatment approaches will most likely become a new standard in relapsed/refractory and front line CLL therapy. The fact that durable responses can be achieved with time limited treatment will not only reduce medical and financial toxicity, but also reduce the probability of resistance development.


Codesign has the potential to transform health and other public services. To avoid unintentionally reinforcing existing inequities, better understanding is needed of how to facilitate involvement of vulnerable populations in acceptable, ethical and effective codesign.To explore citizens’ involvement in codesigning public services for vulnerable groups, identify challenges and suggest improvements.A modified case study approach. Pattern matching was used to compare reported challenges with a priori theoretical propositions.A two‐day international symposium involved 28 practitioners, academics and service users from seven countries to reflect on challenges and to codesign improved processes for involving vulnerable populations.Eight case studies working with vulnerable and disadvantaged populations in three countries.We identified five shared challenges to meaningful, sustained participation of vulnerable populations: engagement; power differentials; health concerns; funding; and other economic/social circumstances. In response, a focus on relationships and flexibility is essential. We encourage codesign projects to enact a set of principles or heuristics rather than following pre‐specified steps. We identify a set of principles and tactics, relating to challenges outlined in our case studies, which may help in codesigning public services with vulnerable populations.Codesign facilitators must consider how meaningful engagement will be achieved and how power differentials will be managed when working with services for vulnerable populations. The need for flexibility and responsiveness to service user needs may challenge expectations about timelines and outcomes. User‐centred evaluations of codesigned public services are needed. Over the 2 days, participants shared case examples of recent service design/codesign applications (many using EBCD) in sectors such as health and social services, employment supports, policing and justice. Our aims were toidentify challenges when working with vulnerable populationscodesign improved approaches through roundtable discussionsformulate a research agenda to advance understandingmobilize and share knowledge about engaging vulnerable populations in codesign and coproduction of public services.This paper outlines the challenges discussed and solutions developed and presents some principles and tactics that codesign facilitators can adopt when working with vulnerable and disadvantaged populations in health and related services.22.1We adopted a modified case study approachEach case is based on practitioners’ experiences of codesign in public services. During the event, three panels of project leads presented a total of 11 illustrative cases of working with vulnerable populations. We present quotes from symposium participants using a code … youth were going into crisis and having to leave the area for treatment. Some youth had to transfer to a different foster home, community, or move to a different province because they'd aged out of youth housing. Some were kicked out of a program [for] not complying with the rules. All cases had challenges establishing initial and sustaining repeated engagement over the course of the projects. Symptoms and life circumstances interfered with some people's ability for prolonged engagement. Projects involving youth with mental health issues noted high dropouts due to health crises, housing transitions and service closures.In the Australian study of adults with mental illness, the greatest challenge was identifying carers  for some adults with mental illness. Only half of the study participants reported having carers, and services were not able to provide accurate, up to date contact information for them, suggesting “a need for specific engagement efforts for carers.” [1T]In the study involving domestic violence survivors, local participants were less willing to come forward and participate because “they were really scared and worried” [6V]. In the young offender study, recruitment proved impossible due to legal anonymity for young offenders prior to age 18, and a reluctance of staff members to act as gatekeepers in the research, “…straight away I got ‘we don't have capacity for this; we're too busy.’” [7V]Box 3.1.2Power differentials were challenging in all of the cases. For example, when working with adults with mental disorders, the Australian study noted that “challenges occurred in the dynamics between service users who had had negative experiences, and staff within working groups” [1T]. Similarly in Scotland, tensions were noted due to dominance of the medical model vs a recovery model that places lived experience of service users at the centre because “… we are questioning that dominant medical world and they aren't liking it—they are struggling with it.” [2V]In England, adults with personality disorders (Case 3) felt highly vulnerable when reflecting on prior experiences of apparent powerlessness. Power issues also had to be negotiated between youth with mental health issues and their former service providers prior to the codesign session (Case 4). Tensions also arose for domestic violence survivors when police services would only permit participation of women within the region of the study (Case 6). Finally, in studies involving Indigenous communities, historical legacies of discrimination and harm, and “a deep on‐going history of colonialism that still persists…within our health care system…,” can influence the acceptance of non‐indigenous researchers and make research difficult in these communities [8V].3.1.3[4V]How and where we offered food and refreshments … we didn't realize it would be problematic, but some youth had eating disorders and felt very uncomfortable eating in front of other people. In several cases , health vulnerabilities affected participation in codesign processes. For example, in the project involving work with domestic abuse survivors, recounting experiences sometimes triggered past trauma. In some studies, unexpected personal issues  interfered with participation in focus groups or codesign meetings. In one case, “a youth participant at a codesign event had discontinued all her medication two days before (cold turkey) and was ill at the event.” [4T] Other health concerns  limited participants’ abilities to fully contribute to codesign discussions, or feel comfortable at events. For example, one researcher explained,3.1.4[5T]Youth with mental health and employment challenges face many barriers to engaging in the healthcare system and sustaining employment. They are focused more on the ‘day‐to‐day’ concerns of life, and may not see immediate value in participating in ‘codesign’ or projects focused on system‐level change. Economic and other social challenges such as difficult home circumstances, being precariously housed or precariously employed, prevented consistent participation for the studies involving youth .3.1.5Working with vulnerable and disadvantaged populations was also highly resource intensive. It took considerable resources and a dedicated research coordinator to reach out, provide information, support travel and build relationships with adults with mental health issues in Australia (case 1) and youth with mental disorders in Canada (case 4). In the young workers’ project, “Building capacity of the youth to participate takes time, patience and nurturing” [5T] to prepare them to participate in the research. In the project for survivors of domestic violence (case 6), significant concerns arose about the ability to allocate sufficient resources to the external team. Securing external resources to bring in designers in order to “dream big” [1T] about possible service improvements and to provide resources for further development and to support implementation was also a challenge in the study of services for adults with mental health issues in Australia (case 1).3.1.6Additional challenges in carrying out codesign work with specific populations included ethical considerations, context and communication. Some study participants shared stories of traumatic experiences that were very upsetting for research team members to hear (case 4). Well‐intentioned research ethics processes inadvertently created anxiety for some vulnerable populations; for example, concerns about trust and exploitation were particularly acute for Indigenous populations (case 8). In mental health contexts, poor communication between services, service users and carers presented challenges in two studies (Cases 1 and 4).Concerns were also expressed that more attention needs to be given to how to support implementation and evaluation of the changes resulting from codesign processes through using approaches such as the critical incident technique,3.2Table We summarize the challenges and principles in Figure 3.2.1Trust, flexibility and responsiveness were identified as important principles in the recruitment processes. Participants recommended that recruitment be built on pre‐existing trusting relationships . In Indigenous communities, it is essential to identify and work with a gatekeeper and take time to understand issues as defined by the community rather than taking an outside perspective.Other key tactics included being responsive to what works for the group, adopting creative ways to reach out, such as targeted social media, engaging “insider” champions, leveraging established networks and engaging natural community‐based groups. In the Young Worker's study, “It was the ‘outside of the box’ … innovative employment providers that were willing to engage in a dialogue about system change” and “appreciated the opportunity to reflect and engage in dialogue.” [5T]Continued engagement requires time to foster mutual understanding, consider unique contexts and motivations, give primacy to the user or group experience, ensure meaning and build capacity see Box . It is e3.2.2Empowerment of service users and power sharing across perspectives was noted as essential and very rewarding,”… what was really amazing was when youth presented their prototypes—family members and service providers were just blown away by what youth had presented”. [4V] specifying shared roles and responsibilities and listening to service user voices throughout codesign processes resulted in “…relationships developing and conversations changing between family members and service providers that had sometimes been adversarial.” [4V]®[8V]As a non‐indigenous person‐ I negotiate my position, my privilege and my power in performing research with indigenous peoples. This … begins with being open to working with and acknowledging the problems and needs of the community first. Formal agreements are often advisable, but an Indigenous research protocol such as OCAPTo avoid unresolvable differences between those at different levels of authority , a recommended tactic was to establish a separate advisory panel representing all perspectives to provide advice and recommendations.3.2.3Creating processes that (a) enable participants to feel safe, (b) establish an environment conducive for codesigning services and (c) recognize the emotional toll that codesigning services can have on participants and researchers were important principles to address health concerns. Principles of engagement can be designed to facilitate open and safe conversation and allow space for venting early on in the process so that later codesign stages can be more productive; this was a specific element in the training delivered in the Australian codesign study. There is also a need to be responsive to participant needs, offer frequent breaks and provide a quiet space (or “chill room”), and emotional support should participants become distressed. Working within existing groups is a suggested tactic to offer natural support.[2V]A lot of health staff seem far more interested in their status and control than in people's lived experience in the end…. people who make decisions … they are particularly uncomfortable about valuing life experience. It is also important to recognize that distress may also be an issue for staff members who may feel quite anxious about meeting clients who are in a position to be critical of their practices.Practitioners need to support staff as well as service users and keep the emphasis on improvement rather than past difficulties. Then, staff have the opportunity to discuss the challenges they are facing. In the ambulance service case, “Staff has really needed to talk about their touchpoints so it was incredibly useful…” [3V].3.2.4[5T]Youth have varying degrees of connection with formal systems and challenging life circumstances as well as episodic mental health issues [that] make it difficult to establish a consistent and meaningful connection. Understanding the history and context of each group and respecting cultural differences enable knowledge to be shared in a culturally safe manner. Specific tactics such as sending taxis to pick up participants and providing videoconferencing or online options for groups whose circumstances make it difficult to engage  may facilitate participation.Similarly, varying meeting times  and offering shorter meetings can maximize participation across several events rather than asking participants to attend every meeting.3.2.5[7V]Because the teams were being disbanded, funding taken away– one person was in a phone call saying “I've got a case load of 12 young people that I have no one to give them to”. And there is me [researcher] going, “Oh can you just find me five young people?” So I decided to withdraw then and say the door is always open … but I am not going to push any further. To garner support from funders for more widespread use of coproduction in service design, participants emphasized the importance of evaluation to demonstrate impact. They also suggested securing champions from the medical community and other professional groups. Since funding support for public services for vulnerable groups is often in flux, practitioners and researchers were advised to be flexible and remain vigilant to embrace opportunities for funding, resources and partnerships that may arise.4The eight case studies illustrate a number of common challenges that were consistent with our theoretical propositions when codesign health and other public services with vulnerable groups and themes that have emerged in prior literature.A cross‐cutting theme was the centrality of relationships to the entire codesign processThe reflections from practitioners of codesign processes with different vulnerable populations offer a set of principles and suggested tactics that others can adopt for service design with vulnerable populations. Practitioners need to be vigilant in protecting vulnerabilities, while simultaneously empowering participants to codesign improvements based on challenging past experiences. Attending to the “human side” can be difficult yet simultaneously the most rewarding part of codesign practice with vulnerable populations. Practitioners must navigate the need for formal accountability while retaining flexible and responsive processes. New understanding is required of “downward” accountability that acknowledges “partnerships and complexity” rather than the “upward accountability” to predetermined organization goals and outcomes that is the traditional logic of many health services.From an institutional perspective, the findings also suggest that the procedures of health‐care organizations and professional regulators can present challenges to researchers doing codesign work. It is essential that good ethics practices protect those sharing experiences, without overwhelming them. Research ethics boards must be supportive of Indigenous research methods and frameworks, and ground rules should be established to ensure cultural safety.Symposium participants expressed appreciation for the opportunity to come together to share challenges and successes to date and to plan for future opportunities to continue to learn together how to improve codesign practice with vulnerable populations. A high priority for future deliberations is how to support implementation of codesigned solutions in service delivery, as an integral part of the design effortsImportant considerations for integrating these approaches into the mainstream way of doing business in health services were resource intensity and planning for the unanticipated. All researchers described this process as resource intensive, requiring intensive efforts by one or more research coordinators for ethics (sometimes at more than one organization), recruitment, continued engagement, data gathering, data analysis and codesign meetings. When considering how to embed coproduction in day‐to‐day health service design, budgets must cover time of designers and offer fair honoraria for participants’ time, with room for unanticipated contingencies.4.1A strength of this work is that the event format allowed for learning from multiple cases of working with vulnerable populations to codesign public services. A limitation is that each case could be further explored in much greater depth to obtain a more fulsome understanding of what worked well and what could be improved. This will be the strategy in future meetings of the event participants. The on‐going international collaborative will play a continuing role in developing practitioner‐led applications of health and social service design and improvement approaches.5Lessons from the eight cases examined at our international symposium suggest that challenges in engagement and power differentials require particular attention when codesigning health and other public services for vulnerable populations. Our analysis prioritizes a set of principles that can enhance engagement and create flexible and responsive codesign processes that are respectful of the readiness of vulnerable populations. In future, greater emphasis is needed to support implementation and user‐centred evaluation of codesigned services to demonstrate effectiveness. Suggested approaches for vulnerable populations can help to overcome stigma, create safe spaces and support participants who might have experienced trauma, while respecting principles of control and access to the knowledge gathered from these communities. On‐going work of the international consortium and future research will better connect civil society in health and social service design, while improving transparency and accessibility of services for all citizens, including those most vulnerable.The authors have no conflict of interest to declare.Each case study had received the necessary ethical approvals where required in their respective countries. All symposium participants completed a video release form giving permission to use their video commentary for analysis and knowledge exchange purposes. The McMaster University Research Ethics Board did not require ethics approval for the symposium, and no original data collected in the individual studies were shared.


The new and rapid advancement in the complexity of biologics drug discovery has been driven by a deeper understanding of biological systems combined with innovative new therapeutic modalities, paving the way to breakthrough therapies for previously intractable diseases. These exciting times in biomedical innovation require the development of novel technologies to facilitate the sophisticated, multifaceted, high‐paced workflows necessary to support modern large molecule drug discovery. A high‐level aspiration is a true integration of “lab‐on‐a‐chip” methods that vastly miniaturize cellulmical experiments could transform the speed, cost, and success of multiple workstreams in biologics development. Several microscale bioprocess technologies have been established that incrementally address these needs, yet each is inflexibly designed for a very specific process thus limiting an integrated holistic application. A more fully integrated nanoscale approach that incorporates manipulation, culture, analytics, and traceable digital record keeping of thousands of single cells in a relevant nanoenvironment would be a transformative technology capable of keeping pace with today's rapid and complex drug discovery demands. The recent advent of optical manipulation of cells using light‐induced electrokinetics with micro‐ and nanoscale cell culture is poised to revolutionize both fundamental and applied biological research. In this review, we summarize the current state of the art for optical manipulation techniques and discuss emerging biological applications of this technology. In particular, we focus on promising prospects for drug discovery workflows, including antibody discovery, bioassay development, antibody engineering, and cell line development, which are enabled by the automation and industrialization of an integrated optoelectronic single‐cell manipulation and culture platform. Continued development of such platforms will be well positioned to overcome many of the challenges currently associated with fragmented, low‐throughput bioprocess workflows in biopharma and life science research. Optical manipulation—which enables highly selective and dynamic processes in micro‐ and nanoscopic systems—has proven to be a versatile and integrated technology throughout many scientific areas. This technology is based on light‐induced electrokinetics that gives rise to designated forces on both solid and fluidic structures. Since the discovery of the optical gradient and scattering forces in 1970 by Ashkin et al.  were developed 11. In addition, the high optical power density causes cell damage over time and limits the duration of experiments. To overcome these limitations, a novel optical manipulation technique known as OETs was developed. OET enables massively parallelized optical manipulation of single cells via the utilization of optical beams to generate patterned virtual electrodes on a photoconductive material  over a much larger addressable area  with the installed Nikon 4×, 0.28NA objective.Conventional and plasmonic optical tweezers have become powerful tools in biology allowing high‐resolution experiments on trapped single cells. However, both are limited to a small manipulation area due to large optical intensity requirements generated via high‐power lasers  in comparison to conventional and plasmonic tweezers (104–106 W/cm2), making them noninvasive to achieve cell control and motion without compromising cell viability. Secondly, the low optical power requirements eliminate the necessity of a high numerical aperture objective to tightly focus a high‐power laser, which otherwise limits the area of particle control and manipulation. OETs significantly increase the manipulation area by two orders of magnitude in comparison to optical tweezers via the utilization of a 10x objective and a light‐emitting diode (LED) as the illumination source, thus facilitating high‐throughput processes  coating the surface to partially drop the voltage, enabling the single‐cell self‐locking function in high conductivity media. A device consisting of 250,000 phototransistor traps over a 1‐cm2 area has been shown to enable simultaneous trapping of over 100,000 polystyrene beads. Furthermore, the device enables the selective release of trapped particle via a scanning light beam as shown in Figure Valley et al.  developeThe advanced OET‐based devices described above offer a wide variety of potential applications, including single‐cell studies involving multiplexed environmental stimuli, high‐throughput, and high‐resolution genetic transfection, study of cell‐to‐cell signaling, tissue engineering, in vitro fertilization, immunotherapy, and beyond. However, these platforms have been limited to proof‐of‐concept experiments at the bench level.32, house air, and optional O2) to operate, as well as an optional Ethernet port. An optical module consisting of an epifluorescent microscope with LED illumination and a custom digital mirror display for creating patterned illumination is situated above a motorized stage in the “sample bay”  in the sample bay. Each WPI acts as a miniature incubator, sized to hold a single 96‐well plate with temperature control (15–40°C) and is supplied with humidified air with specified CO2 and O2 content (0–20%). The WPIs hold separate 96‐well plates which provide both cells and reagents for importing into individual chips. These same WPIs are also used for exporting cells and are designed to keep cells in a suitable culture environment for at least 24 hr to maximize the flexibility of the system and eliminate the need for constant human supervision. The reagent bay holds the media used for on‐chip cell culture as well as reagents for cleaning in between runs. Below the reagent bay is the “waste module” for collecting all liquid waste.The broad potential applications of OET have led to the development of an industrial platform, Beacon®, which incorporates opto‐electro‐positioning (OEP) technology, a variation on the OET technology, into an automated standalone system shown in Figure ” Figure a,b. ThisUnderneath the sample, bay resides the electrical components, which include the computer. Custom software controls all aspects of the system, with the main user interface being a large touchscreen monitor situated just above the sample bay. The chips are fabricated using semiconductor manufacturing technology whereby an array of phototransistors is patterned on a silicon substrate, which will become the floor of the microfluidic channels. Walls are created using photolithography and the ceiling consists of an ITO‐coated glass cover. These three layers are bonded together to form a chip which is mounted on a printed circuit board (PCB) that provides electrical connections as well as an EEPROM for storing identifying details for each chip.Within each chip, there are a series of parallel fluidic channels with rows of NanoPen chambers situated along one side. The NanoPens are photolithographically defined structures that create unswept regions that are protected from shear flow, which can be created in the main fluidic channels by means of a corresponding syringe pump. These NanoPen chambers are connected to the main channels through a small opening . Due to the small scales, the inside of the NanoPens do not experience any convective mixing, rather any mass exchange between the channels and pens is dominated by diffusion. Figure 4The integrated technology has the flexibility and capability to enable a broad array of applications applicable to commercial large molecule drug development, including antibody discovery, clonal selection, gene editing, linking phenotype to genotype, and cell line development. We explored a wide variety of cell‐based discovery and optimization processes while simultaneously developing new assays focused on quantitative data readouts. In particular, we developed techniques for the manipulation and monitoring of isolated individual cells of yeast, hybridomas, B cells, Chinese hamster ovary (CHO), HEK293T, and HepG2. In addition, other groups have demonstrated the ability to select CRISPR edited clones as well as the ability to link phenotype to genotype, both on single cell levels and using T‐cells and tumor cells  via hybridoma technology . The process includes a magnetic negative selection to remove non‐B cells and a FACS‐based positive selection enrichment protocol to enrich for ASCs to address the low‐frequency distribution of antigen‐specific ASCs found in murine spleen and lymph node compartments. Using the tunable OEP parameters and customizable culture conditions on the platform, we effectively isolated single ASCs into nanopens while maintaining their viability. Within an hour of loading the ASCs, we executed two color soluble antigen bead‐based assays screening assays to simultaneously identify IgG producing and antigen‐specific ASCs. The 0.74 nanoliter volume of the nanopens in the OptoSelect™ 3500 chip combined with ASC secretion rates in the 10–1000 s of IgG/sec  that enables direct screening of secreted immunoglobulins from ASCs harvested from hyperimmunized wild‐type mice  assays were developed, either diffusion‐based (in‐pen) or bead‐based (in‐channel), to evaluate IgG secretion levels of both transiently transfected HEK 293‐6E cells  analysis, Figure 8With the capabilities now available for single‐cell sequencing, integrated single‐cell analysis systems like this one will find many applications that link up genotype to phenotype. Two recent examples capitalize on this integration to generate and identify CRISPR edited clones very quickly in an automated manner as well as isolate rare cells for subsequent genotyping.CXCR4 gene, which encodes for a transmembrane receptor protein clinically‐relevant for HIV infection. Homozygously edited cell lines should not express the marker and therefore a fluorescent assay using anti‐CXCR4 antibody was used to identify nonfluorescent clones for selection. Selected clones were exported with a process that splits each clone into two separate exports, one for sequencing and one for proliferation. Expected edits were confirmed by genomic DNA sequencing in some of the selected clones, demonstrating the ability to quickly identify edited clones of interest while simultaneously keeping a live culture ready for scaleup  on a single system allows for full biological workflows to be performed with significantly minimized resources.Digital cell biology on the platform creates the opportunity to transition many of today's cell‐based well plate assays to a unique new format, unlocking a step function increase in workflow scale and speed. Complex and time‐consuming assays, like the measurement of growth and IgG secretion rate on thousands of clones, have proven to be straight‐forward to transfer onto the platform's nanofluidic environment, making them routine to run on a day to day basis. We envision many more complex assays being reduced to routine software‐controlled workflows, such as on‐chip functional assays that require multiple precisely defined populations of cells interacting with reporter cell‐based assays. Examples include plasma B cells combined with reporter cells that indicate if the IgG molecule is functional, T cell activation by dendritic cells, T cell killing of tumor cells, or defined cell number micro‐organoids. In addition, we believe that capture of real‐time assay kinetics of single cells or cell clones across time and across multiple assay types for the same cell population will enable opportunities to discover and rank individual clones that previously relied on single snapshots of the population in time, like FACS and ELISA. Measuring cell surface protein expression, protein secretion, metabolic profile in addition to RNA‐seq from the same individual cell will enable researchers to build deep profiles or cell “fingerprints”, unlocking novel insights at the individual cell level. Combining the power of machine learning and AI with digital cell biology offers additional power to unlock deep insights into mechanistic biology that has thus far proven elusive at the macro scale. This technology can be applied to many areas within biopharma including antibody discovery, assay development, antibody engineering, and cell line development. With the ability to select the right cells, the technology can also be applied in the future to cell therapy manufacturing as well as workflows within synthetic biology, and diagnostics. We believe digital cell biology platforms will prove to be transformative to multiple industries that require a dramatic step forward in speed and scale to realize the next wave of breakthroughs.


Social information networks have the potential to shape the spatial structure of ecological communities by promoting the formation of mixed‐species groups. However, what actually drives social affinity between species in the wild will depend on the characteristics of the species available to group. Here we first present an agent‐based model that predicts trait‐related survival benefits from mixed‐species group formation in a multi‐species community and we then test the model predictions in a community‐wide field study of African savannah herbivores using multi‐layered network analysis. We reveal benefits from information transfer about predators as a key determinant of mixed‐species group formation, and that dilution benefits alone are not enough to explain patterns in interspecific sociality. The findings highlight the limitations of classical ecological approaches focusing only on direct trophic interactions when analysing community structure and suggest that declines in species occupying central social network positions, such as key informants, can have significant repercussions throughout communities. Ecological theory has traditionally viewed community structure as the outcome of direct trophic interactions. We here combine agent‐based modelling of mixed‐species group formation with a field study of African savannah herbivores to show that also social interactions between species, such as social information use, can drive the spatial structure of communities. The study highlights that declines in species occupying central social network positions can have community‐wide repercussions. Ecological theory has traditionally viewed community structure and function as the outcome of direct trophic interactions such as predation, herbivory, and interspecific resource competition Morin . Over thet al. et al. et al. vice versa), and species providing high antipredator benefits may simultaneously incur high resource competition costs, trade‐offs between these costs and benefits will affect patterns in social affinity between species  the proportion of the heterospecific species with whom grouping resulted in higher survival probability than experienced in the typical conspecific group, and (2) the change in survival probability experienced by the focal individual when grouping with the heterospecific species that yielded the highest survival probability compared to when grouping with conspecifics.We systematically varied parameters for the focal and target species to understand how the costs and benefits of mixed‐species grouping depend on species‐specific characteristics Table . We initGazella thomsonii), Grant’s gazelle (Gazella granti), impala (Aepyceros melampus), common warthog (Phacochoerus aethiopicus), ostrich (Struthio camelus), topi , hartebeest (Alcelaphus buselaphus), blue wildebeest (Connochaetes taurinus), plains zebra (Equus quagga), African buffalo (Syncerus caffer), common eland (Tragelaphus oryx) and giraffe  , leopard (Panthera pardus), cheetah (Acinonyx jubatus), spotted hyena (Crocuta crocuta) and black‐backed jackal (Canis mesomelas) , which is part of the larger Serengeti‐Mara ecosystem. The study species were the 12 most common herbivore species of the open plain habitat: Thomson’s gazelle Vigilance . We calculated the mean proportion of time that individuals spent vigilant as no significant effect of the limited variation in group size was found in a general linear model with species included as an independent variable (Table le Table .A)Probability of alarm calling ( was determined from predator simulation experiments (N = 651) in which we presented the study species to life‐sized photostats of their five main predators in the lateral view Relevance of alarm calls ( was quantified from playback experiments (N = 2434 playbacks) Body mass Group size  and a laser rangefinder (Bushnell Scout DX 1000 ARC). Groups were defined by inter‐individual distance < 100 m Diet overlap Habitat overlap  of their sites of occurrence at 500 × 500 m resolution (Pettorelli J)Similarity in movement pattern (migratory/resident) ( was coded as ‘0’ when one species was migratory and the other resident and ‘1’ when both species were either migratory or residents.E)Phylogenetic relatedness Predator‐specific predation pressure Social affinity . Following Godde et al. , and ∑W is the sum of the social affinity indices of all species. The affinity indices were used to create an undirected social affinity network for the study community  homoscedasticity in a plot of fitted versus residual values and (2) the normal distribution of the residual frequency distribution in a QQ plot. We also ran the analysis with the undirected network as the response variable to assess if the results were affected by our approach of directing the network by using empirical data to inform the ABM (see above); the only qualitative difference was that the effect of phylogeny became a tendency rather than statistically significant, confirming the general reliability of the approach (cfr. Table All variables were standardised to range between 0 and 1. In a multiple‐regression approach, the final model was obtained by removing all fixed effects with We calculated the social differentiation index according to Whitehead  using a lme4 (Bates et al. asnipe (Farine All analyses were performed in R v. 3.4 (R Core Team e Farine  loaded.The ABM shows that decreasing vigilance of the focal species is associated with an increase in the proportion of heterospecific species with whom grouping results in a higher survival probability than obtained with conspecifics Fig. a & 5. AnThe ABM also predicts an increased affinity for the heterospecifics with the most informative alarm calls Fig. ; Fig. 4bThe ABM further predicts that intense intraspecific resource competition enhances the attraction to heterospecifics rather than conspecifics as social partners Fig. ; Fig. 4cet al. et al. The ABM moreover shows that the benefits gained from grouping with the most advantageous heterospecific species increases with increasing predator vulnerability of the focal species Fig. b. This pIn contrast to the high survival benefits that more vulnerable species get from grouping with the most advantageous heterospecifics, the proportion of heterospecific species that are preferable to conspecifics as social partners generally decreases with increasing predator vulnerability of the focal species in the ABM Fig. . (Note: et al (In this study, we used multi‐layered social network analysis to test theoretical predictions from an ABM designed to reveal how trade‐offs between detection and dilution benefits and resource competition costs result in assortment of species into MSGs according to their species characteristics. In our empirical study of African savannah herbivores, we found that species characterised by low vigilance had higher propensity to form MSGs, and that MSGs were more often formed with species whose alarm calls elicited strong responses. This is in accordance with the theoretical prediction of higher MSG benefits to less vigilant species and from joining heterospecifics with more informative alarm calls. These findings highlight the importance of detection benefits in promoting MSG formation and that dilution benefits alone are not enough to explain patterns in social affinity. Our study thus demonstrates social information use as a driver of interspecific sociality, in line with the general prediction made by Gil et al  using dyet al Antipredator benefits from MSG formation are furthermore indicated by higher affinity for heterospecifics among smaller, more vulnerable, species. Conceivably, this affinity could also be promoted by a higher cost from intraspecific resource competition in smaller herbivores. Smaller ruminants have a higher rumen turnover rate due to a higher mass‐specific energy requirement (Kleiber , and thiet al. et al. et al. In line with sensitivity to resource competition is also the tendency of the African savannah herbivores to avoid species with overlapping diet. Thus, although our results as a whole point to antipredator benefits as being central in shaping the overall patterns of interspecific social attraction among savannah herbivores, the impact of resource competition costs should not be dismissed. In this context, it should also be noted that we focussed on general patterns in social affinity averaged over one year, and it is likely that seasonal and interannual variation in food availability affects the role of resource competition costs relative to antipredator benefits, with consequences for the compositions of MSGs. However, whereas evidence from the study system indeed shows that patterns in social affinity undergo seasonal changes (Kiffner et al. et al. et al. et al. et al. et al. et al. et al. et al. By documenting the role of social information use in driving interspecific social associations, this study underscores that understanding social behaviour, not only within but also between species, can be of key importance in population and community ecology (Goodale et al. et al. et al. et al. et al. et al. et al. The significant impact that species can have on the survival of each other through their social links has clear implications for conservation management (Snijders JBJ conceived and designed the study with inputs from DWF and KM. Field data were collected mainly by KM and secondarily by JBJ. KM performed the statistical analyses. The theoretical model was developed by DWF with significant input from KM and JBJ. JBJ wrote the manuscript based on a first draft written by KM and DWF. Click here for additional data file.


QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in plant research. We also describe the necessity of standardizing and describing phenotypic studies using the Minimum Information About a Plant Phenotyping Experiment (MIAPPE) standard to enable the reuse and integration of phenotypic data. In addition, we show how deep phenotypic data might yield novel trait−trait correlations and review how to link phenotypic data to genomic data. Finally, we provide perspectives on the golden future of machine learning and their potential in linking phenotypes to genomic features.Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high‐throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus ( This review addresses the state of the art on plant genome sequencing, phenotyping and how to bridge these. Genome sequencing sees a new revolution and phenotyping is becoming extremely important. Arabidopsis thaliana, yeast and Drosophila  or genomic prediction technologies, even within the scope of a single project. Furthermore, machine‐learning and other data science techniques can extract novel insights from meta analyses of multiple datasets. However, there are several obstacles that need to be addressed before this can become widely applicable. This review outlines the current state of the art in genomics, plant phenotyping, and standardization. It explains how these data can be integrated using data science and machine‐learning techniques, and discusses current challenges that are being addressed by the plant science community.Analyses that combine advanced phenotyping and genomic datasets offer great potential for the discovery of novel insights, such as in GWAS  .Examples of long‐read assemblers include Miniasm Li, , Canu Ket al., , SMART det al., et al., et al., et al., The relative costs and high error rate of long‐read technologies negate some of their benefits. Error rate was particularly problematic for long reads from early versions of the third‐generation Oxford Nanopore platform, which offered a read correctness of below 70%  and, less commonly, insertions and deletions (InDels) including copy‐number variations (CNVs). A reduced representation of a genome is potentially the cheapest way to gain SNP and marker information in order to enable genome‐wide association studies (GWAS) and genomic selection studies  to medium coverage resequencing (in the range of 20–40×) is increasingly common for small to mid‐size genomes  accessions together with a wild relative (Oryza rufipogon) to assemble multiple genomes, revealing gene loss and gain , which greatly improves running times for large genomes  or MapMan ontology  imaging with red, green and blue (RGB) cameras Figure , thermalTriticum or Zea. Small pot sizes ensure that there is enough space for many replicates as well as easy handling in automated phenotyping stations, but may also limit plant growth  require considerable experimental space and resources necessary for the growth and analysis of a wide array (>200) of plant genotypes. Proper attention must be given to environmental conditions, ensuring that they are consistent across all replicates. Constant environmental conditions allow for a better assessment of physiological responses and most analyses are typically carried out with plants that are grown individually in pots, either in a growth room with small plants such as Arabidopsis, or in the glasshouse with larger, but agriculturally more relevant species such as et al., et al., et al., Given the important role that the environment plays in plant growth and development, a comprehensive report of environmental conditions during experiments is of paramount importance, both for experiments carried out under controlled conditions as well as in the field  and European Nucleotide Archive (in Europe). Phenotypic data, due to its high divergence, cannot easily be tackled by a highly streamlined and generalized platform. However, in line with the value of original data, funding agencies  does not suffer from ‘p≫n’, i.e. the number of variables  is usually not larger than the number of samples (n). As an example, the Atwell study (2010) recorded 107 diverse phenotypic values in between 90 and 180 accessions or more. Therefore, many techniques from the extensively studied field of gene network reconstruction  found for example phenylpropanoids and myo‐inositol to be predictive for both conductance values.Firstly, as a way to bridge for example well refined molecular measurements such as metabolic profiles to physiological parameters, one can use partial least square (PLS). This technique allows the determination of relationships between outcome variables and predictor variables. Gago et al.  used thiet al.  approach, developed in the van Eeuwijk laboratory  partial correlation analysis that removes the influence of other variables on a variable pair or Bayesian network reconstruction. Common to all these methods is that they try to find relationships between two entities that are not dependent on the other variables. As an example, consider abscisic acid (ABA) that influences both stomatal conductance  but potentially important and causal variables into account. In addition, while these methods do not link traits or physiological variables with the underlying genomic basis (except for QPSO), they do provide structural insights about trait interrelationships. This understanding can be used to modify a target trait by genetically modifying another trait whose genetic basis is already understood. However, it has to be noted that all modelling insights are restricted to the data at hand, meaning many missing variables will make this more difficult.et al., et al., et al., et al., et al., et al., et al., Another valid abstraction approach is to couple phenotypes to genes or genomic regions, leveraging a meaningful phenotypic ontology  or Caffe2 (https://caffe2.ai/). In addition these big data centered companies develop dedicated hardware that promises to greatly accelerate training and analysis tasks. Therefore it is not surprising that plant image data is analyzed using a plethora of machine‐learning approaches  tried to predict phenotypes using classical genomic Best Linear Unbiased Prediction (BLUP) as well as several machine‐learning techniques. The latter clearly outperformed BLUP for yeast with very controlled environments, whereas for wheat and rice, BLUP performed particularly well when there was population structure  the availability of the machine‐readable ontology term‐enriched phenotypic datasets for well defined genes; (ii) the largest wealth of functional data for gene annotation, which is related to the former point; (iii) the use of standardized populations from the 1001 genome consortium, facilitating abstraction at the phenotypic level; and (iv) standardization, driven for example by TAIR. Also, for genetic and genomic studies, it is necessary to note the importance of accurate phenotyping. The most advanced (in terms of crop plants) is most likely maize that, despite its tremendous genetic variety, is tackled in a well planned and standardized way, driven both (pan)genomically  or at least related crops (i.e. Brassicaceae) on a large‐scale basis going beyond simple gene annotation.et al., et al., The impact that the genomics revolution has made on plant science is undeniable and innovative pangenomic approaches that allow the integration of data of related species are beginning to take hold in the plant field. We are therefore in the middle of a genomics data explosion. We are also at an exciting time point, witnessing the next revolution in phenomics (Tardieu The authors declare no conflict of interest.Box 1Plant genome sequencing has evolved to soon become a commodity approach for small genomes.Phenotypic data standardization recommendations are provided by MIAPPE.Many tools and databases facilitate bridging genotypes and phenotypes.Box 2Algorithms working on multiple genomes of a species are still in development.It is still an open question how to best combine short and long reads into assemblies.More rigorous phenotype ontologies and machine‐learning approaches are likely to improve our understanding of plants.


GATA2 deficiency syndromes. Additionally, population studies of common genetic variation have revealed mechanisms by which human hematopoiesis can be modulated. We discuss advances in functionally characterizing common variants associated with blood cell traits and discuss therapeutic insights, such as the discovery of BCL11A as a modulator of fetal hemoglobin expression. Finally, as genetic techniques continue to evolve, we discuss the prospects, challenges, and unanswered questions that lie ahead in this burgeoning field.Hematopoiesis, or the process of blood cell production, is a paradigm of multi‐lineage cellular differentiation that has been extensively studied, yet in many aspects remains incompletely understood. Nearly all clinically measured hematopoietic traits exhibit extensive variation and are highly heritable, underscoring the importance of genetic variation in these processes. This review explores how human genetics have illuminated our understanding of hematopoiesis in health and disease. The study of rare mutations in blood and immune disorders has elucidated novel roles for regulators of hematopoiesis and uncovered numerous important molecular pathways, as seen through examples such as Diamond‐Blackfan anemia and the  Cis‐regulatory elementGenomic regions of transcription factor binding sites and other non‐coding DNA that can influence transcription of a nearby gene. Examples include promoters, enhancers, and silencers.Common variant association studies (CVAS)Genetic studies which aim to identify common variants  associated with a phenotype of interest.Congenital dyserythropoietic anemia type II (CDA II)The most common subtype of a group of rare hereditary disorders characterized by congenital anemia, ineffective erythropoiesis, the development of secondary hemochromatosis, and uniquely among CDA II, an abnormal glycosylation of erythrocyte membrane proteins.Diamond‐Blackfan anemia (DBA)A rare inherited bone marrow failure syndrome characterized by normochromic macrocytic anemia, limited cytopenias of other lineages, low reticulocytes, and decreased erythroid precursor cells in the bone marrow.EosinophilA type of white blood cell that plays important roles in fighting certain parasitic infections, and is also implicated in conditions such as allergies and asthma.EpistasisInteractions between genetic loci in their effect on a trait, such that the impact of a particular genotype depends on the genotype at other loci in a non‐independent manner.Expression‐quantitative trait locus (eQTL)Associations of DNA sequence variation with changes in gene expression.Familial platelet disorder with predisposition to myeloid leukemia (FPDMM)RUNX1 gene, clinically characterized by low platelet count, abnormal platelet function, and an increased risk of developing other blood disorders or cancers such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML).A rare inherited blood disorder caused by mutations of the Fanconi anemia (FA)A heterogeneous genetic syndrome associated with risk of congenital malformations, bone marrow failure, and cancer.Genome‐wide association study (GWAS)A genetic analysis that tests for genome‐wide associations between genetic variants and a phenotype of interest.HaploinsufficiencyThe phenomenon in which a single functional copy of a gene is insufficient to maintain normal function.HeritabilityThe proportion of variation in a particular trait that is attributable to genetic factors.ImputationThe use of linkage patterns in a more densely sequenced reference panel to predict unobserved genotypes in a study dataset.LinkageThe nonrandom association of alleles at different loci.Myelodysplastic syndrome (MDS)A heterogeneous group of malignant hematopoietic stem cell disorders characterized by dysplastic and ineffective blood cell production and a risk of transformation to acute leukemia.NeutropeniaA decrease in circulating neutrophils.PleiotropyA phenomenon in genetics whereby a DNA mutation or variant has an effect on multiple traits.PolycythemiaAn increased hemoglobin concentration and/or hematocrit in peripheral blood.Polygenic risk scoreA weighted sum of the number of risk alleles for a phenotype carried by an individual, where the risk alleles and their weights are usually defined by association loci and their effect sizes detected from genome‐wide association studies.Population stratificationSample structure due to differences in genetic ancestry among samples.Rare variant association studies (RVAS)Genetic studies which aim to identify rare variants  and their effects on a phenotype of interest.Sickle cell disease (SCD)A monogenic blood disease caused by a glutamic acid to valine substitution in the β‐globin chain of normal adult hemoglobin, which causes polymerization of mutated sickle hemoglobin and deformation of red blood cells under conditions of deoxygenation.Thrombocytopenia‐absent radius (TAR) syndromeA rare congenital syndrome primarily characterized by limb anomalies and low platelet counts.ThrombocytopeniaA low number of platelets in the blood.β‐ThalassemiaA group of autosomal recessive hereditary anemias characterized by reduced or absent beta‐globin chain synthesis, leading to alpha‐ and beta‐chain imbalances that cause clinical manifestations of hemolytic anemia and impaired iron handling.Every second, each one of us produces millions of diverse circulating blood cells—including erythrocytes, platelets, and leukocytes—through the coordinated process of hematopoiesis Fig A–C. ThisGata1 were found to have defective erythropoiesis  and rare  variant association studies, each employing different approaches to work up their variants of interest. Common variant association studies (CVAS) usually take the form of genome‐wide association studies (GWAS), in which individuals are genotyped using arrays that capture mostly higher‐frequency variants. Statistical analyses can then be used to determine whether each variant is associated with a continuous or binary phenotype of interest. CVAS focus on traits with polygenic architectures comprised of many variants with small individual effects and usually include a large proportion of healthy individuals in the study population. Notable current limitations of CVAS include its high multiple testing burden from evaluating millions of variants, its inability to capture a substantial portion of heritability, and the difficulty of functionally characterizing association signals  often require alternative analytical methods, since single‐variant analysis can be underpowered to detect associations if the individual mutation is too rare in the study population. To counteract this, burden tests have been developed, which collapse many variants within a gene or region into a single risk score. This approach thus performs a per‐gene or per‐region association study as opposed to per‐variant association tests in GWAS ‐of‐function coding variants segregating within families with hematologic traits at extremes of the phenotypic distribution  nicely illustrate how rare variant genetics have illuminated our understanding of human hematopoiesis and how this process can be perturbed in disease in unexpected ways. DBA is an inherited hypoplastic anemia in which erythroid precursors and progenitors are selectively reduced in the bone marrow, while other lineages are ostensibly produced normally . In 1999, linkage analysis of six separate families with FPDMM revealed that all pedigrees contained heterozygous mutations in RUNX1  and acute myeloid leukemia (AML) in affected individuals, and demonstrated a key link between RUNX1 haploinsufficiency and predisposition to malignant hematopoiesis ; loss of dendritic cells, monocytes, B, and natural killer (NK) cells (DCML deficiency); and familial MDS and AML  syndrome identified biallelic mutations in et al, et al, et al, et al, While many of the examples discussed above emerged through traditional family‐based linkage or sequencing analyses, as larger cohorts of rare disease patients are being assembled, broader assessments through RVAS and gene burden analyses are occurring. Such approaches have been valuable in the context of DBA , but also are independent risk factors for a multitude of non‐hematological diseases, including leukocyte count for coronary heart disease , enabled the discovery of genes and TFs important for the stage‐specific regulation of hematopoietic differentiation, and provided insights into how distinct hematopoietic lineages can be co‐regulated by pleiotropic variants acting in multipotential progenitor populations  has been shown to be a key modifier of the major β‐hemoglobin disorders, sickle cell disease, and β‐thalassemia, where it is able to ameliorate symptoms through replacement of the mutated adult β‐hemoglobin  and CVAS, when in reality, there is likely a continuum of genetic effects in human traits  exhibits extensive clinical heterogeneity, ranging from mild phenotypes that remain undetected for decades to severe forms with multiorgan damage and early mortality . Only by considering this complete spectrum of allelic variation can we begin to explain all of the nuances and variation observed in blood disorders.Another example of this convergence can be seen in mutations altering GATA1 activity or function both globally and at specific loci. On one hand, GATA1 bound cis‐regulatory elements (CREs) are frequently impacted by common genetic variation associated with hematopoietic traits, but these variants primarily tune the activity of such CREs with effect sizes below what is required to cause frank disease  serve as a prime example of this endeavor. PRSs are a weighted sum of risk alleles carried by an individual, in which the risk alleles and their weights are defined by their effect sizes on a phenotype of interest. In many complex traits and diseases, PRS can already quantify risk more accurately than current clinical models  Mapping the full allelic spectrum of how genetic variation regulates hematopoiesis in health and disease.(ii) Expanding genetic studies to populations from more diverse ancestries.(iii) Improving the resolution and scalability of efforts to characterize the functional mechanisms by which genetic variants impact hematopoiesis.(iv) Development and implementation of genetic risk scores to improve blood trait predictions in clinical settings.https://www.ebi.ac.uk/gwas/homehttps://clinicaltrials.gov/ct2/show/NCT03282656Table EV1Click here for additional data file.Table EV2Click here for additional data file.