Almost all regulatory processes in biology ultimately lead to or originate from modifications of protein function. However, it is unclear to which extent each mechanism of regulation actually affects proteins and thus phenotypes. We assessed the extent of N‐terminal protein truncation in a global analysis of N‐terminomics data and find that most proteins have N‐terminally truncated proteoforms. Because N‐terminomics analyses do not identify the process generating the identified N‐termini, we compared identified termini to the three N‐termini generating events: protein cleavage, alternative translation, and alternative splicing. Of these, we sought to identify the most likely cause of N‐terminal protein truncations in the human proteome. We found that protease cleavage and alternative protein translation are the likely cause for most shortened proteoforms. However, the vast majority (about 90%) of N‐termini remain unexplained by any of these processes identified to date, so revealing large gaps in our knowledge of protein termini and their genesis. Further analysis and annotation of terminomics data is required, to which end we have created the TopFIND database, a major systematic annotation effort for protein termini. We outline the new features in version 3.0 of the updated database and the new bioinformatics tools available and encourage submission of generated data to fill current knowledge gaps. Protein products of a gene can be largely variable. From 20061 human proteins ; termini predicted from the biochemical and structural characterization of the protease and its substrates (designated here “cleavage” termini); termini predicted from alternative translation events found by global translation initiation sequencing stored in TISdb 3We analyzed human N‐termini observed by terminomics screens and compared these to N‐termini inferred from cleavage events, alternative translation, or alternative transcription as annotated in TopFIND, by counting the overlap between the instances of N‐termini in each group. Counting N‐termini in a position‐specific and not an experiment‐specific manner, we avoided recounting the same N‐terminus multiple times—although this does underestimate cleavage events where two or more proteases cut at the same site—as it is the case when, for example, cleavage is facilitated by protein structural features such as in flexible N or C terminal protein sequences, linker regions between domains, or in exposed loops on or between domains. We identified 48095 observed or inferred N‐termini in the human proteome. Focusing on N‐termini that do not correspond to the canonical start site of the protein (i.e. carboxyl to position > 3 to account for initiator methionine processing plus one exopeptidase or diaminopeptidase event), we identified 23915 observed and inferred N termini as shown in Fig. We then collapsed together N‐termini if they are close (distance < 3 amino acids) to avoid recounting the same terminus multiple times that might be due to proteolytic ragging by exopeptidase activity in vivo. Again, this may underestimate the number of distinct termini due to independent cleavage events by the same or different proteases within the 3‐residue cluster. Focusing on observed N‐termini, we identified 9843 N‐termini clusters that contain at least one observed N‐terminus across the full length of the protein. Notably, 7409 of these were internal in the protein (again carboxyl to position > 3 with the remaining 2434 clusters at positions 1–3) and mostly were equally distributed along proteins as shown in Fig. 4We next investigated how many observed N‐termini were explained by inferred termini in TopFIND. As described above, inferred N‐termini are predicted from a reported cleavage, an alternative spliced transcript start site, or an alternative translation start site reported at the position in question. An experimentally observed N‐terminus identified at the same position as an inferred terminus was considered to be explained by at least one N‐termini generating process. Of the 7409 internal clusters, only 933 were explained in that they had an associated evidence for an inferred terminus Fig. C. ConseqIn the clustered data, most of the 933 explained N‐termini clusters (849) fell close to a protease cleavage site Fig. D. This eThe above observations hold true when analyzing individual datasets, as shown in Table 5Protein cleavage and chain truncation has historically been underestimated, mostly because proteases were considered as enzymes involved principally in degrading proteins and not as precise proteolytic processing devices 6http://clipserve.clip.ubc.ca/topfind/topfinder), queries the database for a list of input termini simultaneously and compiles a report that contains termini evidences, general protein and protein domain information, as well as protease statistics for the termini TopFINDer, a new open access tool in TopFIND (http://clipserve.clip.ubc.ca/topfind/pathfinder) takes the cleavage and inhibition information from TopFIND and queries the protease web for paths between a query protease and a set of input cleavage sites (for example a list of termini from TopFINDer). The resulting paths are sequences of cleavage and inhibition interactions between proteases and their inhibitors that provide insight as to which intermediate inhibitors and proteases might have been indirectly involved in generating the protein truncations identified when studying a protease. Taking all identified paths together, PathFINDer ultimately reports an experiment‐specific network summarizing all identifying paths. These paths and the involved intermediate proteases and inhibitors represent valuable new avenues for hypothesis generation. Thereby, the workings of the network can be validated by targeting intermediate proteins biochemically by chemical or genetic inhibition or knock‐down as reported To address the challenges in protease substrate assignment posed by the complexity of the protease web the open access software tool PathFINDer (7Our present analysis using TopFIND v3.0 has assessed the state of knowledge of the N‐terminome. The pervasiveness of N‐terminal truncations throughout the proteome highlights the importance of both seeking and understanding the effect of protein truncations and the processes generating neo‐termini. This will benefit both an in‐depth understanding of protein and cell biology as well as for the development of targeted therapeutics that avoid clinically relevant drug side effects from unrelated off targets and family member counter targets or anti‐targets. With the complexity of phenotypes of cells and organisms, complex patterns of deep regulation are expected to be at work. However, it remains to be investigated which of the mechanisms of regulation at play have the greatest impact on the phenotype. In addition, truncation of proteins could also be the reason why certain proteins and their peptides are not observed by mass spectrometry. Knowledge of these alternative N‐termini could increase the detection of proteins with proteomics screens using archetypical peptides, SRMs or antibodies. Indeed, if antibodies or SRMs are deployed to target parts of a protein from only the analysis of the sequence, e.g. N‐ or C‐terminal sequence stretches, without considering known cleavage or translation sites, this will lead to systematic false negative results if these regions are present in some conditions but proteolytically removed in others. Therefore, in such cases, the presence and absence of proteins cannot be reliably assessed without experimental knowledge of the population of N‐ and C‐termini of proteins.To understand and probe complex networks of regulation in the future, data will need agglomeration to then generate specific hypothesis for experimentation. PathFINDer is one such new tool to assist in these efforts. However, the network so far only considers a subset of protease cleavage and inhibition associations and does not yet incorporate kinetic information. In the future we anticipate further refinements of the model to provide more specific and biological meaningful analyses with higher predictive power.In summary, we assessed the amount and genesis of protein truncation observed experimentally and found that it has a great impact on the majority of proteins in the proteome. Protein truncation is a special protein modification in that it is irreversible and so sets proteins on a path of no return. As compared to alternate translation and splicing, which are also irreversible, protein processing by proteases has very immediate consequence to the phenotype. Thus, we expect protein cleavage to be a quick response to stimuli and for secreted proteins, this is one of the last opportunities for a cell to modify a protein as leaves the cells’ realm of influence.The authors have declared no conflict of interest.


Journal of Cellular Biochemistry Published by Wiley Periodicals Inc.The endo/lysosomal system in cells provides membranous platforms to assemble specific signaling complexes and to terminate signal transduction, thus, is essential for physiological signaling. Endocytic organelles can significantly extend signaling of activated cell surface receptors, and may additionally provide distinct locations for the generation of specific signaling outputs. Failures of regulation at different levels of endocytosis, recycling, degradation as well as aberrations in specific endo/lysosomal signaling pathways, such as mTORC1, might lead to different diseases including cancer. Therefore, a better understanding of spatio‐temporal compartmentalization of sub‐cellular signaling might provide an opportunity to interfere with aberrant signal transduction in pathological processes by novel combinatorial therapeutic approaches. J. Cell. Biochem. 117: 836–843, 2016. © 2015 The Authors.  ARL8BADP‐ribosylation factor‐Like 8BBMPRbone morphogenetic protein receptorEGFRepidermal growth factor receptorGEFguanine nucleotide exchange factorGLP‐1Rglucagon‐like peptide‐1 receptorGPCRsG protein—coupled receptorsHGFhepatocyte growth factorIQGAP1IQ motif containing GTPase activating protein 1LAMTORlate endosomal/lysosomal adaptor and MAPK and mTOR activatorMethepatocyte growth factor receptorMVBmultivesicular bodiesmTORmechanistic target of rapamycin kinasemTORC1mTOR kinase complex 1PDGFRplatelet‐derived growth factor receptorPAC1Rpituitary adenylate cyclase 1 receptorPTHRparathyroid hormone receptor typeRTKsreceptor tyrosine kinasesSTAT3signal transducer and activator of transcription 3TGFtransforming growth factorTSCtuberous sclerosis complexTSHRthyroid‐stimulating hormone receptorV2Rvasopressin type 2 receptoren route to lysosomes. By a third mechanism, signaling components are exclusively localized to endosomes/lysosomes but not directly connected to receptor endocytosis.Cells respond to different environmental stimuli by initiation of signal transduction at the plasma membrane. The binding of ligands to specific receptors at the cell surface, such as Receptor Tyrosine Kinases (RTKs) or G protein—coupled receptors (GPCRs), triggers the activation of many downstream signaling pathways, which are important for normal tissue homeostasis. For integration and regulation of complex signaling networks the endo/lysosomal system is essential [Miaczynska et al., The general principle of spatio‐temporal regulation of receptor‐mediated signal transduction is that the cellular response to different types of ligands is maximal and transient at the plasma membrane and sustained in endosomes. In this review we try to look at cellular signaling from an organelle‐centric point of view and present selected examples of deregulation of endosomal signaling in disease progression such as cancer. Hence, we discuss also perspectives in development of combinatorial therapies based on our current knowledge on compartmentalized signal transduction.Endocytosis of cell surface receptors is one of the control mechanisms of signal transduction initiated by extracellular stimuli. For a long time it has been assumed that receptors signal from the plasma membrane until they are internalized, endocytosed and sent to lysosomes for degradation. Stimulation of cells in vitro with appropriate ligands as, for instance, EGF reaches maximal EGFR activation levels within the first minutes of stimulation [Stasyk et al., Notably, different ligands can have diverse effects on recycling of the same receptor. Again the EGFR is a well‐established example for this. The receptor is directed for lysosomal degradation if induced by EGF but is recycled upon transforming growth factor (TGF)‐α stimulation. TGF‐α leads to sustained EGFR signaling and, therefore, is more mitogenic than EGF [Waterman et al., Signaling from endosomes has been demonstrated for a number of cell surface receptors from different receptor families such as the RTKs , serine/threonine kinase receptors (transforming growth factor‐β (TGF‐β), the bone morphogenetic protein (BMP) and the activin receptors), GPCRs, toll‐like receptors, as well as interferon, Wnt and Notch receptors. Endosomal signaling of these receptors is well characterized and was extensively reviewed elsewhere [Hupalowska and Miaczynska, There are several important characteristics of endosomal signaling that is spatially and temporally separated from signaling at the plasma membrane: 1) signaling complexes on organelles are different from those at the plasma membrane; 2) receptor endocytosis and active signaling from organelles are required for the full activation of their downstream effectors; and 3) there could be specific targets or distinct pathways stimulated by the same receptor depending on which endosome it is localized. These properties of endosomal signaling were very recently shown for Hepatocyte growth factor (HGF) receptor (Met) signaling from two different populations of endosomes in human breast cancer models [Menard et al., Scaffolds and adaptor proteins often organize specific endosomal signaling complexes. For example, such complexes containing activated endocytosed EGFR are organized on early endosomes by APPL, which recruits AKT and its substrate GSK3 [Miaczynska et al., Another well‐established example is activated transforming growth factor‐β receptor (TGFβR), which upon internalization interacts with Smad anchor for receptor activation (SARA) on early endosomes. In case of bone morphogenetic protein receptor (BMPR) another specific scaffold, endofin, organizes signaling from endosomes. These and many other scaffolds that make possible activation of their downstream targets at specific subcellular locations, were previously comprehensively summarized in [Palfy et al., An interesting mechanism of early endosomal EGFR signaling, sustained by the non‐receptor tyrosine kinase PTK2B/PYK2, was reported recently [Verma et al., Recent data suggest that GPCRs mediate the production of cyclic AMP not only from the plasma membrane but also from endosomal membranes. Originally, two studies have shown that two GPCRs, thyroid‐stimulating hormone receptor (TSHR) [Calebiro et al., All examples discussed above, of specific endosomal signaling complexes, contain internalized and endocytosed receptors of different families and scaffolds specific for different receptors and (sub‐)populations of endosomes. In addition to this well established and commonly accepted type of endosomal signaling there is an emerging field of organelle signaling independent from endocytosis, if the latter one is defined as active transportation of cell surface components into the cell. In most eukaryotic cells the plasma membrane makes up only for a minor part of all cellular membranes. The endo/lysosomal system, as a component of cellular endomembranes, provides membranous platforms to assemble specific signaling complexes at specific subcellular locations. Here we will briefly discuss endolysosomal signaling of the mechanistic  target of rapamycin (mTOR) kinase.Endolysosomes are the fusion product between late endosomes and lysosomes and the place where most of the hydrolysis of endocytosed cargo takes place [Huotari and Helenius, It has become evident already some time ago that endosomes play a role in cell migration [Sadowski et al., Another interesting example of endosomes as vehicles of signals over long distance is transportation of activated STAT3 from the plasma membrane into the nucleus upon activation with EGF and PDGF [Bild et al., Above‐mentioned examples from different fields compose quite a significant body of evidence for spatial and temporal consequences of endosomal signaling. It is particularly exciting task for the future to demonstrate different physiological responses produced by activated receptors at the cell membrane and at endosomes. Better understanding of how to specifically interfere with the two waves of signaling might be beneficial for therapeutic purposes to treat different diseases, including cancer.Deregulations of signal transduction at different subcellular levels, caused by defective trafficking of growth factor receptors, can drive tumorigenesis Table . MutatioOne well‐established oncogenic deregulation of cell surface receptors is their escape from ligand‐stimulated ubiquitination by the Cbl family of adaptor proteins and ligases that function as negative regulators of many signaling pathways. Such mechanism was described for EGFRvIII, which is the most common mutation of EGFR gene. This tumor‐specific deletion in the extracellular domain of EGFR contributes to the formation of many epithelial malignancies. In some brain tumors this mutation of EGFR occurs at extremely high frequency. Interestingly, although EGFRvIII possesses only about 10% of the intrinsic activity of wild‐type EGFR its net signaling rate is enhanced by the delay of its endocytosis. The low level of EGFRvIII signaling causes hypo‐phosphorylation of the receptor that prevents engaging of Cbl and, therefore reduced polyubiquitination and degradation of the receptor, and, therefore, increased recycling. This may also play a critical role in the development of resistance to tyrosine kinase inhibitor treatments as observed in the clinics [Han et al., Aberrant activity of GPCRs is frequently associated with tumorigenesis. Recent deep sequencing studies show that GPCRs are mutated in nearly 20% of human cancers [O'Hayre et al., Upregulation of lysosomal mTORC1 signaling is one of the most common hallmarks of human cancers [Zoncu et al., Since patients often do not respond to conventional anti‐cancer drugs or develop resistance, alternative therapies are required. According to the current sequential protocol, the patient is administered one by one to different drugs, for example the tyrosine kinase inhibitors, until the optimal response is reached. Unfortunately the risk of multidrug resistance in this approach is increased. An alternative therapeutic approach by administering combinations of different drugs at the same time could provide a cure for patients that did otherwise not respond to conventional therapies. Appropriate combinations should potentially enhance response and decrease development of drug resistance. Combinations of well‐established drugs, which inhibit receptors on the cell surface with specific inhibitors of endosomal signaling as well as more general inhibitors of endocytosis, which act on different levels of the process such as internalization, recycling or degradation see Fig.  might opMet signaling from late endosomes was recently shown to be crucial for sustained Rac1 activation in breast cancer cells, responsible for cell spreading and metastasis formation [Menard et al., Another combinatorial approach could be the simultaneous inhibition of several receptors or the targeting of common signaling pathways, in the context of crosstalk between different receptors. As discussed above, EGFinduced early endosomal PYK2 signaling, which leads to PYK2‐STAT3‐Met positive feedback [Verma et al., All those inhibitors of endocytosis are still pretty far from preclinical development since they might target too common cellular mechanisms with potentially high toxicity at the organism level. However, the mode of action with targeting endocytosis would suggest that chemical libraries could be developed in high‐contents screening setups that act like molecular chaperons by selectively only disturbing endocytosis and recycling of certain mutated oncogenic receptors.H. pylori eradication in the clinics and have also been used recently in tumor models. Proton pump inhibitor pretreatment inhibited V‐type H+‐ATPase activity and increased both extracellular pH and pH of lysosomal organelles. Hence, in human/mouse xenograft models oral pretreatment with proton pump inhibitors is able to sensitize human solid tumors to anticancer drugs [De Milito and Fais, Margalef et al. have shown recently that inhibition of the endosomal V‐ATPase is a potential therapeutic strategy for the treatment of colorectal cancers with mutant BRAF, which is predictive of poor prognosis and therapeutic resistance [Margalef et al., An approach combining the mTORC1 inhibitor Everolimus with an aromatase inhibitor improved progression‐free survival in patients with hormone‐receptor‐positive advanced breast cancer [Baselga et al., We anticipate that selective targeting of the endosomal signaling, especially in combination with conventional anti‐cancer therapy and targeted small molecules, may offer more effective treatments. The here suggested link between endosomal signaling and cancer increases expectations from this type of combinatorial therapeutics in future.


In this data article, we determined the concentration levels of heavy metals including Pb, Co, Cd, Mn, Mg, Fe and Cu as well as selected anions including  Specifications TableValue of the data•Data can be used as a base-line data for concentration levels of some metals in herbal distillates.•Data shown here may motivate further studies on medical benefits of herbal distillates due to their low concentration levels of metals.•Data shown here may serve as benchmarks for other groups working in the field of pharmacology and toxicology.1In the data, characteristics of plants used for extracting herbal distillates are presented in 2Twenty different herbal distillates of the most used and popular herbal distillates were purchased from herbal distillate distribution shops in Bushehr, Iran. All purchased herbal distillates were produced by traditional methods from Ordibehesht Company in Meymand city, which is the main city in Iran for herbal distillates production. All herbal distillates bottles were stored in a dark place at room temperature in their original sealed plastic containers until the analysis. Before taken for analysis, samples were collected in 100 ml sterile glass bottles that were previously washed and dried in oven at 180 °C. The concentration levels of heavy metals and anions in herbal distillates samples were determined using flame atomic absorption spectrometry  and a spectrophotometer  respectively. The limit of detection (LOD) was calculated as


CDH1 mutations is high in families with hereditary diffuse gastric cancer (HDGC). Men and women have a 70% and 56%, respectively, cumulative risk of developing diffuse gastric cancer by age 80. Women additionally have a 42% cumulative risk of developing breast cancer. Due to the high penetrance of these mutations, prophylactic total gastrectomy is currently recommended for CDH1 mutation carriers. However, whether everyone with a CDH1 gene mutation is at risk for HDGC is not clear.The reported penetrance of germline Mutation identification was performed by next‐generation sequencing. Mutations and variant status was confirmed by Sanger sequencing in 11 family members.CDH1 mutations. The first family carries a novel truncating, nonsense CDH1 mutation that we were able to trace for three generations, but reports no family history of diffuse gastric cancer. The occurrence of cancer in this family deviates significantly from the expectation for HDGC. The proband from the second family presents with breast cancer and carries a previously reported pathogenic CDH1 mutation, but also reports no family history of diffuse gastric cancer.We present two families with pathogenic CDH1 mutation penetrance in order to better counsel asymptomatic CDH1 mutation carriers on preventative measures and general care.Our study demonstrates the need for further analysis of  E‐cadherin  gene are associated with the autosomal dominant cancer susceptibility syndrome, hereditary diffuse gastric cancer (HDGC)   is another gene that is assessed in some of these panels. ATM maps to chromosome 11q22‐q23  and ATM (NM_000051). Sanger sequencing was performed by a commercial laboratory in 11 family members to confirm mutation and variant status.Next‐generation sequencing was performed by commercial laboratories to identify mutations in a panel of breast cancer‐related genes. Mutations or variants of unknown significance were identified in We conservatively estimated the number of people expected to have developed gastric cancer in a family of six members with the age distribution of Family 1 using published penetrance estimates . This mutation has not been previously reported in the literature. It is located in coding exon 3 (of 16 coding exons) and results in a change from the amino acid glutamic acid at position 58 to a stop codon (p.E58*), ultimately resulting in the loss of exons 4–16.The truncating CDH1  carries a p.Q64* mutation  in CDH1 c.172G>T mutation: the proband's mother (70‐years‐old), brother (47‐years‐old), maternal aunt (57‐years‐old), and two daughters (aged 29 and 39‐years‐old), and maternal grandfather (93‐years‐old)  from the 2.36 expected in a family with this age distribution.We compared this low rate of cancer in this family with the expected number of gastric cancers in HDGC families , one of lymphoma, one of lung cancer, and one of rectal cancer. The proband's family speculates that the large amounts of cancer could possibly be due to the family being downwind of nuclear testing in the 1940s and 1950s. The familial CDH1 mutation has been identified in individual III‐7, a 69‐year old male with squamous cell skin cancer whose sister and mother both died of breast cancer.ATM the proband carries is a C to A substitution at nucleotide 4964. This results in the replacement of a serine at codon 1655 with a tyrosine. These two amino acids have dissimilar properties, though it is not clear what the effect of this mutation would be on the ATM protein (Data S1). The mutation was also found in the proband's mother, but not in the proband's brother or grandfather (Data S2). We speculate that it came through the proband's maternal grandmother and may explain her diagnosis of Non‐Hodgkins lymphoma at age 50 and the proband's maternal great uncle who died in his 80's of a brain cancer with unknown pathology. The family reports no cancer on her father's side and he tested negative for both mutations ; this mutation disrupts the splice donor site. This mutation has been previously reported in a family with predominantly lobular breast cancer cases and one early onset gastric cancer case  OR three confirmed individuals with gastric cancer in first or second degree relatives regardless of age OR a single case of gastric cancer before 40 or personal or family history of gastric cancer and lobular breast cancer, one diagnosed before 50  indicates family members with the ATM p.S1655Y/c.4964C>A variant of unknown significance. (−) indicates tested noncarriers. The legend illustrates cancers affecting the family.Click here for additional data file.


The current literature on the influences of family environment on childhood obesity is predominantly based on western populations and has focused on the role of parents. This study examined the influence of grandparents on the development of obesity among Chinese primary school aged children.n = 99) and explored perceived causes of childhood obesity. The cross-sectional study examined the association between children’s objectively measured weight status and reported health behaviours, and the presence and role of grandparents in the household. It included children from three randomly selected third grade (8 to 10 years) classes from each school (n = 497).A mixed methods study was conducted in four socioeconomically distinct primary school communities in two cities of southern China. The qualitative study  involved parents, grandparents, school staff, and food retailers in the vicinity of the schools , than children who were mainly cared for by their parents or other adult. Children who lived with two or more grandparents in the household were more likely to be overweight/obese than children who did not live with any grandparent .Grandparents were commonly perceived to contribute to childhood obesity through inappropriate perception , knowledge , and behaviour (e.g. overfeeding and indulging through excusing the children from household chores). Conflicting child care beliefs and practices between grandparents and parents, and between grandparents and school teachers, were felt to undermine efforts to promote healthy behaviours in children. In the cross-sectional study, children who were mainly cared for by their grandparents were more likely to be overweight/obese ; and to consume more sugar-added drinks and unhealthy snacks (Involvement of grandparents in childcare is an important factor contributing to childhood obesity in China. Future preventive interventions should include strategies that target grandparents. Childhood obesity is a pandemic, associated with physical and psychological morbidity in children, as well as contributing to an increase in non-communicable chronic diseases (NCDs) and premature mortality in adulthood . Over thThe influence of the family and home environment on children’s health behaviours is well established. Parenting style, such as rewarding desirable child behaviours using unhealthy foods –16 or wiWe conducted a mixed methods study to investigate the impact of grandparents on the childhood obesity epidemic in China, in order to inform the development of culturally relevant childhood obesity intervention programmes.This mixed methods study includes both a qualitative and quantitative element. While the former gives greater depth, the latter offers greater breadth, so inferences from both parts of the study can be triangulated (to confirm) and complement each other . First, Ethical approval for both parts of the study was obtained from the Life and Health Science Ethical Review Committee at the University of Birmingham.The qualitative study was conducted between December 2009 and May 2010 in two cities of southern China: Guangzhou (GZ) and Hechi . Data coWe identified key stakeholders relevant to children for each school community. Participants were invited by identity group to attend focus groups, to ensure discussion of shared experiences . These iSchool teachers assisted in purposively identifying and recruiting participants in their respective school communities following a pre-defined recruitment strategy that aimed to maximise gender balance and the diversity of participants’ socioeconomic backgrounds. Informed consent (with information on study purpose and the roles of voluntary participants) was sought for all participants. A minimum of five participants with at least two males and two females took part in each of the 17 focus groups.n = 95 participants) were held within the schools and consisted of two sessions, each lasting for approximately 90 min  with school principals were run at the offices of the principals and each lasted for around 45 min. Discussions focused on the broad topic of perceived causes of child obesity. To better enable discussions from the unique perspective of school leaders, questions were phrased as ‘barriers’ that schools had encountered in promoting healthy eating and physical activity on campus and ‘what schools want/need’ for playing a better role in children’s healthy behaviour promotion  who were in the same schools as those from which we recruited the participants for our qualitative study. This data was collected as part of the routine student health surveillance programme, in the same school year. Measurements were undertaken by trained health professionals working for the Education Bureaus, following standardised anthropometry measurement protocols . In eachWe asked two questions specifically about the role of grandparents. First, we asked whether any grandparents live in the household, and secondly, whether grandparents play a role in caring for children (by asking who the child spends most of their time with after school during the weekdays), irrespective of whether or not they live in the household.The main outcome was child weight status. Children were categorised into overweight/obese and non-overweight groups using the age and sex specific WHO 2007 child growth reference values . The dieMultivariable regression analysis was used to examine the relationships between the presence and role of grandparents and 1) child weight status, 2) frequency of unhealthy snack consumption and 3) the likelihood of engaging in a daily minimum of 60 min MVPA. As well as socio-demographic variables, including child sex, age in months, and mother’s education level (proxy measure of socioeconomic position), we adjusted for school (as a fixed effect) and birth weight (shown prospectively to be related to child weight status) , 44 in aNinety five participants 42 male) took part in 17 focus groups (15 in GZ) and four school principals participated in the personal interviews .‘Fat means wealthy’ (Grandparents from HC).A recurrent theme in all groups was an affection and preference for fat children among grandparents.‘My mother loves seeing my daughter getting big…I said not so much meat and snacks and she should learn swimming but she doesn’t understand and thinks I am wrong…’ (A mother from middle class in GZ).‘I said to my son you need to lose weight, he replied that grandma said I am just strong…only you want me to’ (A mother from lower class in GZ).This belief among grandparents often conflicted with the views of parents who did not always share the sentiments:‘We don’t understand what the figures mean …we can’t influence grandparents’ opinion when they believe that the overweight kid is normal weight; but a formal health report may do’.Another common theme in all groups was the lack of recognition of obesity and overweight in children, particularly among grandparents. Assessment of weight status was often done by comparison with other children, and norm setting was among their peers. Many participants considered the annual measurement of children in schools to be meaningless, and they did not understand the reports sent home. As one father commented:‘My parents feed lots of meat to my daughter who is already overweight. They say the “3 highs”  do not affect children, as they are the burden of adults…children can eat freely’.Another common theme emerging from the parent and teacher FGs was the belief that grandparents know little about the health consequences of overeating. Similarly they are unaware of the benefits of a healthy diet. One mother from a middle class area in GZ city said:‘I told my boy his diet needs some improvement…my mum said she is happy with his diet, pretty healthy…not picky, not wasteful… eats almost everything…eats enough meat and enough oil is used in cooking…’. ‘In their time, meat and oil were treasures so now they feel the more the better’. ‘I decided to move out with my wife and son…his grandparents were a big problem…we couldn’t change anything when we lived together’.Parents and teachers (with children) from all sample schools shared the belief that grandparents hold a mistaken perception of what constitutes a healthy diet in children.‘In my childhood, sisters and brothers fought to eat at meal times simply because there were so many children but insufficient food…now each child is cared for by 4 to 6 adults… the single family treasure receiving too much love and attention…I wish to change this situation but it is hard to avoid overfeeding the child by grandparents’.The single-child family structure was discussed by all as a contributor to obesogenic behaviours. Family members and school staff commented that having only one child at home makes the promotion of healthy eating difficult especially when a grandparent is living with them. As one parent said:‘They buy snacks for the child when he/she has behaved well…sometimes in a secret way as I don’t allow snacking…but I can’t manage my parents’.It was frequently discussed that grandparents overindulge their single grandchildren, thus undermining the efforts of parents and school teachers in promoting healthy eating. One parent noted:‘When collecting children, grandparents often bring a sweetened drink or dessert…we educate our pupils don’t snack too much…children remember they will get something after school so some of them don’t eat school lunch properly’.And a teacher commented:‘Now a 9 year old child doesn’t know how to make his own bed…he knows grandma wouldn’t let him do this’. ‘My parents told me how many physical tasks they undertook in childhood; so let the only child enjoy a pain-free childhood…I should respect parents’ opinion’.In addition to the influence on dietary habits, grandparents were considered to over protect grandchildren from physical household chores, thus limiting their activity levels. Several parents made comments on this issue:Questionnaires were completed by 508 of 554 parents invited (response rate = 91.7 %). A total of 497 child/parent dyads were included in the analyses. Among all the participating children, 228 (45.9 %) of them lived with at least one grandparent, and 87 (17.6 %) were mainly cared for by a grandparent . These patterns varied by child socioeconomic status and sex. Live-in grandparents were more common among families with more educated mothers compared to those where mothers had no higher degree (48.5 versus 42.0 %) and among boys compared with girls (49.4 versus 42.1 %). Grandparents as carers were more common among girls compared with boys (18.4 versus 16.9 %) and among families with less educated mothers compared to those where mothers had higher degree (20.8 versus 15.3 %). Overall, approximately a quarter of the children were overweight or obese. Among the four socioeconomically distinct sample schools, the combined prevalence was higher in the upper socioeconomic communities than in the middle and lower socioeconomic ones.B = 2.13 and standardised coefficient Beta = 0.15). Thus, children who were mainly cared for by a grandparent consumed over two more servings of unhealthy snacks per week in comparison with children who were mainly cared for by their parents or other adults. In terms of physical activity, we did not find any association between the role of grandparents and children’s likelihood of engaging in a least 60 min of daily MVPA.Living with at least two grandparents in the same household  and being primarily cared for by grandparent(s)  were significantly associated with child overweight/obesity , indulging behaviour (e.g. overfeeding and sparing the ‘single family treasure’ from household chores) and poor health knowledge . They also counter the attempts by parents and school staff to promote healthy eating and physical activity in children. These attitudes and beliefs largely stem from the historical context of famine and poverty in China during their childhood, where being slim represented poverty and poor health. In support of the qualitative findings, having grandparents living in the household and grandparents taking on a main carer role for children were both associated with increased risk of overweight/obesity in our cross sectional sample. Children who were mainly cared for by a grandparent also consumed unhealthy snacks and drinks more frequently.Our findings show that grandparents are an important influence on children’s weight status, partly through limited understanding of the consequences of and risk factors for obesity and also through a desire to over-indulge their single grandchildren. This is in keeping with findings from a previous small qualitative study in Beijing, which reported that within three-generation households, grandparents overfed and pampered grandchildren through food . The stuThe phenomenon that Chinese children are exempted from household chores but under high expectation to perform well academically was also reported in a previous cross-sectional study . This caMost of the explanations for the mechanisms by which grandparents contribute to the childhood obesity epidemic are also similar to those reported in other studies. Poor knowledge of the health effects of overeating or unhealthy diet in children among carers has been implicated in qualitative studies among mothers in Australia and North America , 56. OurThis is the first qualitative study in China to explore the views of a wide range of stakeholders on causes of childhood obesity. Participants from a variety of socio-economic backgrounds provided views from a broad perspective and this allowed data saturation to be reached. Several steps were taken to ensure data trustworthiness, and we have provided a transparent description of the methods and analysis approach. The cross-sectional study used objective anthropometric measures to assess children’s weight status. A published estimation (based on WGOC reference norm) of overweight and obesity prevalence among Guangzhou’s 6- to 15-year students in the same year  was simiThere were also limitations to this study. China is a vast country with varying geographic conditions and dietary traditions, thus our findings may not be generalisable to other parts of the country. One limitation of the cross-sectional study was that children’s diet and physical activity behaviours were assessed by parental reports. However, a review of methods for assessing physical activity patterns in children concluded that parent-proxy reports were more accurate than children’s self reports .Informal childcare, mainly provided through grandparents, is a growing social trend internationally . In ChinThis mixed-methods study has identified grandparents as important targets for obesity prevention interventions. Findings from the qualitative study indicate strategies and components that can be pursued within intervention programmes.


DAA) for hepatitis C virus (HCV) infection have achieved high cure rates in many patient groups previously considered difficult‐to‐treat, including those HIV/HCV co‐infected. The high price of these medications is likely to limit access to treatment, at least in the short term. Early treatment priority is likely to be given to those with advanced disease, but a more detailed understanding of the potential benefits in treating those with mild disease is needed. We hypothesized that successful HCV treatment within a co‐infected population with mild liver disease would lead to a reduction in the use and costs of healthcare services in the 5 years following treatment completion. We performed a retrospective cohort study of HIV/HCV‐co‐infected patients without evidence of fibrosis/cirrhosis who received a course of HCV therapy between 2004 and 2013. Detailed analysis of healthcare utilization up to 5 years following treatment for each patient using clinical and electronic records was used to estimate healthcare costs. Sixty‐three patients were investigated, of whom 48 of 63 (76.2%) achieved sustained virological response 12 weeks following completion of therapy (SVR12). Individuals achieving SVR12 incurred lower health utilization costs (£5000 per‐patient) compared to (£10 775 per‐patient) non‐SVR patients in the 5 years after treatment. Healthcare utilization rates and costs in the immediate 5 years following treatment were significantly higher in co‐infected patients with mild disease that failed to achieve SVR12. These data suggest additional value to achieving cure beyond the prevention of complications of disease.New direct‐acting antivirals ( BHIVABritish HIV AssociationHCVhepatitis C virusNHSNational Health ServiceRBVribavirinSVRsustained virological responseUKCHICUK collaborative HIV cohortUSSultrasound scansHepatitis C virus (HCV) is estimated to have infected over 170 million people worldwide, accounting for 3% of the global population Several studies have reported higher usage of healthcare services such as hospitalizations and emergency room visits in co‐infected individuals than amongst HIV‐infected patients We aimed to investigate whether HIV/HCV‐co‐infected patients who were successfully treated for mild hepatitis C had reduced usage of healthcare services and costs after completion of successful treatment.Patients were eligible if they attended the study clinic between 1 January 2004 and 1 March 2013. Patients included for analysis required (i) confirmed positive HIV antibody status, (ii) evidence of HCV infection, and for this study, patients being positive for HCV RNA on more than one occasion and (iii) to have received and completed at least 3 months of treatment for HCV between 1 January 2004 and 1 March 2013. This would allow us to obtain at least 1 year of follow‐up for all patients by the date of data collection, 1 March 2014. Patients were included regardless of treatment type which included pegylated interferon , ribavirin (RBV) and latterly protease inhibitors (PI). Analysis was limited to patients without evidence of significant fibrosis to avoid confounding by the fact that patients with more advanced disease have greater healthcare costs and that those with most advanced disease respond less well to therapy Data on patient characteristics, clinical data and healthcare utilization were collected from clinical records supplemented by electronic records for investigations and hospital attendance. Data collected independently by UK collaborative HIV cohort (UKCHIC) Baseline patient information for the entire HIV/HCV‐co‐infected cohort included the patient's age, gender, race, fibrosis/cirrhosis status, baseline laboratory data comprising of CD4 count, HCV genotype, HCV and HIV viral loads, fibroscan results and biopsies. Baseline analysis was then repeated for SVR and non‐SVR groups to allow comparison between cohorts once individuals were identified. For both groups, additional information on treatments given and the precise dates of treatment completion were obtained from patient records.Patients with mild liver disease who received a course of PEG‐IFN and RBV +/‐ protease inhibitors in line with the British HIV Association (BHIVA) guidelines were considered for medical service utilization analysis vs SVR patients. Statistical significance was determined at P < 0.05 estimated using two‐sided Student's t‐tests. To fully assess the benefits of attaining an SVR, we used mean costs as the factor of comparison. Healthcare service costs were obtained from the Department of Health using most recent reference costs, 2012–2013 We assessed differences in healthcare utilization by comparison of rates per‐patient year of follow‐up of each healthcare service. We followed this by calculating total utilization rates over the 5 years and compared total usage per‐patient year between SVR and non‐SVR groups. Risk ratios were then determined for non‐SVR A total of 63 co‐infected patients with mild liver disease received and completed at least 3 months of antiviral therapy between January 2004 and March 2013. Table Table P = 0.0022). Likewise, significant differences were seen in the average number of clinic visits over the course of the study with SVR and non‐SVR using the service 1.1 and 2 times per‐patient year, respectively (P = 0.0018). Those not achieving SVR were more likely to have an ultrasound scan and a fibroscan in the initial 5 years following treatment with a relative risk (RR) of 14.93  and 10.40 , respectively. There was an associated increase in relative risk with the use of all listed healthcare services in the absence of SVR; however, results for hospital admissions and A&E visits did not prove statistically significant.We then investigated how the use of these services varied between groups over the follow‐up period. Figure To ascertain the financial benefits of attaining a SVR, we calculated total costs for resource utilization. Table The study found that within a HIV/HCV‐co‐infected population with mild disease, unsuccessful treatment is associated with significantly higher costs (£1155 more per year) of healthcare utilization per‐patient following HCV therapy than those who were successfully treated. Outpatient and clinic attendances were higher in non‐SVR patients when compared to those achieving SVR  in comparison with non‐SVR group £1489/£2155, 69%). A greater proportion of costs were attributable to hospital admission in those who failed treatment. Of the minority of patients who failed treatment, none had developed severe fibrosis or cirrhosis throughout the duration of the study and so healthcare analysis was not influenced by progression of disease. No significant difference was seen in the number of bloods taken between both cohorts reflecting the fact that both cohorts would continue to be monitored for their HIV irrespective of treatment response. It is also worth noting that although the total cost spent on inpatient services  was higher for non‐SVR patients (£471 per‐patient) than SVR patients (£91 per‐patient), the rates for inpatient services were very low for both groups . It is not possible to estimate the extent of this issue within this study although it may lead to an underestimate of the changes in health utilization. In addition, this study did not consider pharmacy costs of HIV and other drugs received during the follow‐up period, which too will have contributed to the overall healthcare costs for both cohorts.The results from our study add to existing data informing the cost‐effectiveness of antiviral therapies. Whilst we cannot yet know whether successful DAA therapy will have the same benefits, it is likely that the benefits will be similar but further, ideally larger, studies are required. It is possible that the difference between SVR and non‐SVR groups will change with a longer period of follow‐up, but it is likely that there will be greater divergence as disease progression in the non‐SVR group will require more frequent monitoring.In conclusion, this study was the first to compare the impact of successful HCV treatment on healthcare utilization in a HIV/HCV‐co‐infected population with mild disease. Our results show significant differences in healthcare costs and utilization rates between individuals that are successfully treated for HCV compared to those failing treatment, despite the fact that they remain in secondary care.The study provides data in addition to the known benefits of SVR in reducing the risk of cirrhosis, hepatocellular cancer, end‐stage liver disease and disease transmission


The meeting brought together the Indian scientific community and investigators from other countries working on various aspects of chromosome stability. The maintenance of chromosome stability depends on the precise duplication of the genome, efficient DNA repair and recombination, and proper interactions between the centromeres/kinetochores of the duplicated chromosomes and the spindle apparatus Fig. . Errors Accurate DNA repair and recombination is critical for chromosome stability. Jim Haber  discussed genome stability during repair of a broken chromosome in budding yeast. Double‐strand breaks (DSBs) can be repaired by nonhomologous end‐joining (NHEJ) or by homologous recombination in which a intact, identical, or nearly identical sequence is used as a template. However, even conservative repair of DSBs by homologous recombination is associated with a highly elevated risk of mutation. Such mutations often have a “signature” associated with slippage or template switching of the repair DNA polymerases. His group showed that pairs of such inter‐chromosomal template switching events can occur between ectopic  homologous sequences as often as once every 100 repair events. These types of instability associated with ectopic recombination may underlie some of the complex rearrangements seen in human developmental diseases or in cancer cell chromosomes exhibiting chromothripsis in which individual chromosomes are shattered and then reassembled. Eric Alani  continued with the theme of homologous recombination between diverged DNA sequence in yeast. He discussed how cells make the decision to either unwind and reject recombination intermediates containing mismatches (heteroduplex rejection), or to maintain the intermediates and correct the mismatches. He showed that overexpression of the mismatch repair protein Msh6 can decrease or even stimulate heteroduplex rejection, depending on whether the recombination occurs in the context of a replication fork or independent of it. Thus, even though higher levels of Msh6 may improve recombination fidelity in general, this protein appears to reduce recombination fidelity during replication.The identification of genomic regions prone to instability due to mitotic homologous recombination is important. Tom Petes  described evidence that spontaneous mitotic crossovers in yeast are often initiated by a break in unreplicated DNA and presented genome‐wide mapping of mitotic crossovers in yeast. Analysis of mitotic crossover hotspots showed that they are often associated with closely‐linked inverted repeats. Jennifer Surtees  summarized her analysis of the mismatch repair complex (Msh2/Msh3) on expansions of trinucleotide repeat (TNR) tracts in yeast. She showed that msh3 mutations result in a reduction in tract expansions, and proposed a model by which the Msh2/Msh3 complex stabilized small DNA loops to promote tract expansion. These results demonstrate unforeseen consequences of active MMR in the context of TNR tracts and have important implications for understanding diseases caused by TNR expansions.The above talks discussed the potential of homologous recombination to generate genome rearrangements and instability. Wolf Heyer  discussed how recombination has evolved as a pathway with metastable, reversible intermediates to avoid inappropriate DNA strand invasions in non‐allelic targets and thus minimize the potential for genomic instability. Using in vitro assays, he demonstrated how the anti‐recombination helicase Srs2 dissociates the strand invasion catalysed by Rad51‐ssDNA filaments, whereas Topoisomerase 3 reverses D‐loops exerting anti‐recombination activity. These results suggest that recombination and repair pathways should not be seen as a fixed sequence of events, rather as displaying reversibility at multiple steps. Pathway reversibility creates novel circumstances where synthetic lethality can potentially be exploited in targeting recombination pathways during anti‐cancer therapy. Sathees Raghavan  discussed DNA damage and chromosomal instability in mammalian cells with a focus on the less‐studied mitochondrial DSB repair pathway. He showed that Microhomology Mediated End Joining (MMEJ) or alternative‐NHEJ are the preferred pathways for rejoining DNA with DSBs in mitochondria.M. tuberculosis and M. smegmatis in response to hypoxia. Misexpression of Ung in M. smegmatis using a hypoxia‐responsive promoter decreased C to T mutations but compromised bacterial survival.Defects in DNA repair and recombination pathways cause diseases through genome instability. In the EMBO lecture, Ashok Venkitaraman  described evidence that tumors arising in carriers that are heterozygous for a tumor suppressor gene are not necessarily the consequence of the “two‐hit” model of Knudson. More specifically, he found that in a murine model for KRAS‐driven pancreatic cancer heterozygous for a mutation in BRCA2, the wild‐type allele remained active in all of the tumors. Similarly, in human patients carrying germline BRCA2 mutations, the wild‐type allele remained active in ∼75% of cases. These results argue that some tumors are a consequence of haplo‐insufficiency or trans‐dominant effects of the mutant allele. Ganesh Nagaraju  in his talk and Kumar Somyajit in his poster described that distinct complexes of mammalian RAD51 paralogs protect nascent DNA at stalled replication forks and mediate replication restart. B. J. Rao  outlined the non‐random spatial positions of chromosomes in mammalian nuclei and demonstrated dynamic positional changes exhibited by select gene‐rich chromosomes during the DNA damage response. Umesh Varshney  discussed genome stability in Mycobacteria that possess G + C rich genomes. Because of their habitat in the hypoxic environment of host macrophages, their genomes are at increased risk of cytosine deamination (to uracil) and other forms of DNA damage. He showed that contrary to what was expected, there was a remarkable down‐regulation of Ung (a highly conserved class of uracil DNA glycosylases) in During meiosis, DSBs are deliberately inflicted on the genome to promote shuffling of genetic material by homologous recombination and proper chromosome segregation. Bernard de Massy  reported ChIP‐seq experiments showing that the zinc finger protein PRDM9 binding sites are not only sites of meiotic H3K4 methylation (associated with DSBs) but also meiotic recombination hotspots, thus confirming that PRDM9 is the primary determinant of where DSB initiation occurs in the mammalian genome. Once the initiating DSBs are formed, chromosomes must encounter the homolog to recombine. This is facilitated by rapid chromosome movements, which require connections between telomeres and the cytoskeleton. Akira Shinohara  showed in yeast that phosphorylation of Mps3 re‐localizes it from the centrosome to the nuclear envelope during meiosis, facilitating telomere‐led chromosome movement. Meiotic chromosomes are organized into a series of loops that are tethered to a linear axis containing meiosis‐specific chromosomal proteins. As homologs pair, these axes are conjoined into a structure called the synaptonemal complex (SC). The steps of meiotic recombination occur in the context of the axis. K. Muniyappa  described biochemical and structural studies of the conserved chromosome axis protein Hop1, which binds DNA and promotes interactions between pairs of DNA molecules, consistent with a role in coordinating DNA loops in tethered loop‐axis structures. Michael Lichten  described how the conserved Sgs1(BLM) helicase/Top3‐Rmi1 strand decatenase complex regulates meiotic recombination pathway choice. He showed that the Sgs1/Top3‐Rmi1 complex prevents aberrant recombination intermediate formation and directs meiotic recombination intermediates towards two alternative pathways. These include, early resolution as non‐crossovers, or capture by SC‐associated proteins that promote the regulated stabilization of intermediates and their later resolution into crossovers. Nishant K. T.  described the impact of mutants of Msh4, one of these SC‐associated proteins, on obligate crossover formation and chromosome segregation. He showed that the obligate crossover is not protected from variations in crossover frequency and analyzed the contribution of achiasmate chromosome segregation mechanisms.Arabidopsis conferred by loss of two important chromatin‐modifying activities: ARP6, a member of the protein complex that loads histone H2aZ onto chromatin; and DUET, a PHD domain‐containing protein that specifically binds dimethlyated H3K4.Three presentations focused on the roles for chromatin modification in the regulation of gene expression and progression during meiosis. Paula Cohen  described work on small non‐coding RNAs and their associated Argonaute proteins in regulating gene silencing of the unpaired arms of the X and Y chromosomes during mouse spermatogenesis. Aushaq Bashir Malla  in his poster showed that IP6K1, a member of the inositol phosphokinase family, is essential for maintaining genome integrity and orchestrating chromatin remodelling during spermatogenesis, and as a consequence this protein is essential for male fertility. Imran Siddiqi  described meiotic defects in Meiotic recombination is not without its hazards, and Lucas Argueso  described the development of a model system, in budding yeast, to study non‐allelic homologous recombination. The assay uses engineered yeast chromosomes to simulate what transpires in humans when non‐allelic meiotic recombination occurs between large Low Copy Repeats (LCRs), resulting in germline recurrent copy number variation associated with human genomic disorders such as autism.S. cerevisiae (e.g. human pathogenic yeasts) to analyze centromere structure and function. Candida albicans, unlike S. cerevisiae, harbors unique centromeric regions on every chromosome. When a native centromere is deleted, neo‐centromere formation takes place at a centromere‐proximal region. However, gene conversion occasionally copies an unaltered native centromere to replace the neo‐centromere. CENP‐A loading at these centromeres is linked to replication fork stalling indicating that repair proteins may have a role to play in maintaining centromeres. Joseph Heitman  spoke about the role of centromere linkage in the evolution of the MAT locus in Cryptococcus species from a tetrapolar type to a bipolar type. In C. amylolentus, with a tetrapolar MAT configuration, both MAT loci were found to be centromere‐linked. The presence of similar retro‐transposable elements in all centromeres in most Cryptococcus species suggests a role for centromere‐mediated recombination events in this process. Harmit Malik  described how centromeric proteins are rapidly evolving and that most are under positive selection. An illustration of their rapid evolution is that CENP‐A proteins from even closely related species of Drosophila fail to function when heterologously expressed in another species.In addition to accurate DNA repair and recombination, chromosome stability also requires proper assembly of physical structures comprising kinetochores on the centromeric DNA. Kaustuv Sanyal  in his talk and Neha Varshney in her poster described the utility of working with yeasts other than The talks on centromere function and evolution were followed by talks on the regulation of kinetochore function. Tapas Manna  in his talk and Geethu Emily Thomas in her poster provided evidence that the EB1 protein decorates the microtubules on the plus end. It does so by interacting with the Ska complex proteins and forming a ring around microtubules in vitro. Ajit Joglekar  addressed how unattached kinetochores trigger the spindle assembly checkpoint. He showed compelling evidence that the position of spindle assembly checkpoint (SAC) proteins at the kinetochore is important for its activation. The Dam1 kinetochore complex acts as a barrier and does not allow SAC proteins to interact with the spindle pole body component (Spc105) required for SAC activation.A better understanding of the molecular mechanisms that determine stable transmission of genetic material over many generations is critical for understanding how diseases such as cancer arise. Several talks in this meeting highlighted how mechanistic insights into the DNA repair and recombination process or dynamic kinetochore‐microtubule interactions during chromosome segregation can improve human health. The meeting provided an important platform for Indian Principal Investigators and students to engage with the international scientific community on themes related to chromosome stability. We expect future sequels of this meeting will further contribute to the growth of this community in India and its integration with the rest of the world.


The world’s oceans are undergoing rapid, regionally specific warming. Strengthening western boundary currents play a role in this phenomenon, with sea surface temperatures (SST) in their paths rising faster than the global average. To understand how dynamic oceanography influences food availability in these ocean warming “hotspots”, we use a novel prey capture signature derived from accelerometry to understand how the warm East Australian Current shapes foraging success by a meso-predator, the little penguin. This seabird feeds on low trophic level species that are sensitive to environmental change. We found that in 2012, prey capture success by penguins was high when SST was low relative to the long-term mean. In 2013 prey capture success was low, coincident with an unusually strong penetration of warm water. Overall there was an optimal temperature range for prey capture around 19–21 °C, with lower success at both lower and higher temperatures, mirroring published relationships between commercial sardine catch and SST. Spatially, higher SSTs corresponded to a lower probability of penguins using an area, and lower prey capture success. These links between high SST and reduced prey capture success by penguins suggest negative implications for future resource availability in a system dominated by a strengthening western boundary current. Remote sensing of environmental data including sea surface temperature (SST) and chlorophyll Accelerometry has shown great potential to provide fine-scale information on the activity of wild animals. Machine learning algorithms have been applied to recognise patterns in acceleration data, providing robust links between the behaviour of animals and their movement profiles, such that behaviour can be determined remotely67Western boundary currents are a significant source of global heat transport, advecting warm water from the tropics to temperate latitudesEudyptula minor) is the world’s smallest species of penguin and has a breeding colony at Montague Island, off southeast Australia . Montague Island is situated halfway across the continental shelf, with surrounding waters heavily influenced by the dynamics of the EAC and its eddy field  understand the temporal variability of prey capture success by little penguins determined using accelerometry, and assess how this variability was related to the EAC; 2) understand spatial variability in foraging location determined using GPS, and assess how environmental features dictate the way that penguins use available foraging habitat; 3) assess spatial variability in prey capture success determined from GPS, accelerometry and depth recorders in relation to the EAC. We discuss the insight that our findings give into the relative availability of low trophic level species to predators in the context of western boundary current intensification.The field study was conducted on Montague Island , 9 km off the southeast coast of New South Wales, Australia, in September, November and December 2012–2014. This period covers the peak of the little penguin’s breeding season, which can be highly asynchronousThe night before a penguin went to sea, it was caught in its nest box and equipped with a GPS logger  modified with epoxy resin to withstand pressure at depth. The loggers were inserted into heat shrink tubing, then attached to feathers on the lower back with cloth tape , positioned so as to reduce drag but not impede tail movement. These tags were 43 mm in length, 27 mm in width and 13 mm in height, and weighed 55 g in air and 17.4 g in seawater. A range of sampling frequencies was used over the study period to adjust the trade-off between battery life and spatial resolution. For penguins expected to perform single day trips , sampling frequency ranged from 7 – 45 s. For birds expected to perform multiple day trips (incubating birds and birds with larger chicks), the sampling frequency ranged from 30–115 s, however at these sampling frequencies the loggers were still rarely able to record complete multiple days, so spatial analyses were restricted to single day trips. When penguins returned from a foraging trip they were recaptured in their nest boxes, loggers removed and the penguin was weighed in a calico bag using a spring balance scale .Accelerometer data loggers  were attached immediately in front of the GPS units (towards the head) on the middle back for a subset of penguins from November 2012. These tags were 40 mm in length, 28 mm in width and 15 mm in height, and weighed 7.8 g in air and 2.3 g in seawater. The accelerometers recorded acceleration in 3 axes: anterior-posterior (surging), lateral (swaying) and dorso-ventral (heaving) with a range of + /−2 g. The accelerometers recorded depth, temperature and acceleration and were programmed in two modes: “shallow” mode  where parameters were recorded every 10 seconds, and “dive” mode (>1.5 m) where the same parameters were recorded at 30 Hz.Combined tag weight for penguins that were equipped with both accelerometers and GPS was 62 g in air and 19.7 g in seawater, which is < 5% and < 2% of mean bodyweight (~1100 g) respectively. Handling time was kept to a minimum, and in most cases was less than 5 min for both deployment and retrieval of devices. All animal research protocols were carried out in accordance with guidelines approved by the Macquarie University Animal Ethics Committee .et al.2021We previously developed a motion signature to identify prey capture by wild penguins at sea, using a support vector machine algorithm that identified prey handling by wild penguins with a false positive rate of 0.09%. A thorough description of this method and its validation in the wild is detailed in Carroll We assessed temporal patterns of prey capture success by breeding little penguins between November 2012 and December 2014. All available accelerometry profiles were used in this analysis, from both single and multiple day foraging trips. The penguins in this study were not individually marked, so it is not known whether they were resampled in multiple years. However, only 9 birds of the same sex from the same nest were sampled more than once (13%). We used the mean number of prey caught per 90 min period across a foraging trip as an index of prey capture success for that trip. As we might expect penguins to adjust their foraging effort to the availability of prey, we also calculated a measure of catch per unit effort (CPUE), which was the mean value across a foraging trip of the number of prey caught per 90 min window as a function of time spent diving below 1.5 m within that window. We used the mean value over discrete time windows rather than a daily value, as this allowed for comparison among foraging trips of different lengths. We tested a range of time windows  on a subset of eight pooled single and multiple day foraging trips and found that 90 minutes was the window that minimised the standard deviation of the mean foraging trip CPUE (see a (OC3) and geostrophic velocity  and ESA (ENVISAT) satellites) from the Integrated Marine Observing System (IMOS) Data Portal (http://imos.aodn.org.au/imos/). Daily SST and Chlorophyll a data were obtained at a location 5.5 km offshore (east) from Montague Island  in November and December 2012–14 and September 2013–14 (accelerometry data was not collected during September 2012). This offshore location is halfway between Montague Island and the edge of the continental slope where the EAC is centredo S, 150.4 oE) and rotated 19-degrees to be in the alongshore direction.To assess the temporal influence of the EAC on foraging success, we first described relationships between different environmental variables to find a suitable means of representing EAC penetration. We obtained measurements of satellite-derived SST (MODIS-Aqua), chlorophyll a from the same location, and geostrophic current velocity  and chlorophyll a concentration decreased with warmer water . Due to these correlations we chose not to model the effect of more than one of these environmental variables on foraging success simultaneously, although they are each likely to explain a portion of its variance. We chose to use offshore SST as a single proxy for penetration of the EAC, as the EAC brings warm water down Australia’s southeast coast from the tropics in a series of highly variable mesoscale eddies, rather than a continuous southward-flowing stream10a, and occurs at a higher sampling frequency (daily) compared to geostrophic velocities, which are calculated from satellite altimetry data and collated and interpolated over a 10-day cycle.Using linear regression we examined the relationship between offshore SST, chlorophyll To characterize seasonal patterns of EAC penetration, we plotted a time series of daily SST values offshore from Montague Island for 2012–2014, and applied a 10-day rolling mean to smooth the data. To place our findings in a longer-term context, we calculated the mean SST for each calendar day over a period of 11 years (2003–2014). We also calculated the mean SST for each month that penguins were tracked.We used generalised additive models (GAMs) with Gaussian error distributions to estimate the relationship between SST and our two measures of foraging success (mean number of prey caught per 90 min window and CPUE). For each penguin foraging trip, we averaged SST over a four-day window centred on the trip dates. If the foraging trip was longer than four days, we used the mean over the length of the trip. This helped to reduce gaps in satellite data arising from cloud cover, but was still relevant for penguins foraging on short temporal scales.We used locations recorded by GPS loggers to determine the relationship between spatial habitat use and SST. For these analyses we only used single day foraging trips, as these were comparable in terms of the maximum distance that the penguins travelled from the island (~25 km per day). By focusing on single day trips, we were also able to use the most complete GPS tracks, as tracks of multiple day foraging trips were often incomplete due to limitations in GPS battery life on these small loggers.2 cells spanning the penguins’ potential single day foraging range (25 km north and south of Montague Island and east to the shelf edge). The 1 km2 grid was the finest resolution available for the remote-sensed MODIS-Aqua SST data. We averaged SST over the days when we tracked penguins . We chose this method after testing two others that masked relationships between SST and foraging success: a) taking the mean of SST for all days within the range of dates that penguins were tracked (e.g. 3rd – 11th September) and b) averaging over 15 days regardless of the tracking date range (15 days being the longest tracking period).To determine the relationship between foraging location and SST, we created a grid with 1 km2 grid, resulting in counts of locations within each grid cell that we summed for each sampling period . To avoid artificially over-sampling in some areas where penguins rested at the surface, and under-sampling in other areas where gaps were recorded in the GPS data due to the penguins spending more time underwater, we linearly interpolated the raw GPS location data at regular 10 min intervals. Interpolation also allowed us to homogenise the different GPS sampling frequencies used during the study period. We determined a 10 min sampling frequency to be the most appropriate as little penguins travel at a mean speed of 1.8 m/s2 areas that penguins moved through without foraging would get on average a single count (or fewer if the penguin was moving more quickly), whereas areas where they encountered prey and engaged in area restricted search were likely to contain substantially more observations.We spatially binned locations recorded by the GPS tags onto the same 1 kmWe analysed the relationship between SST and penguin location counts using a hurdle model2 grid cell from the mean SST of all grid cells). We compared three measures  and SST anomaly ) in separate hurdle models and compared them using Akaike’s Information Criterion (AIC), to best capture the relationship between SST and both penguin presence/absence and the number of observations within grid cells. We created a visual representation of the relationship between foraging location and SST by overlaying raw GPS tracks on a map with spatial SST anomaly (pixels were coloured according to how much they deviated from the mean temperature of the study area).To test whether penguins are responding to relative SST or absolute temperatures, we assessed both SST and SST anomaly  in relation to the prey caught through the course of single day trips. We also determined the mean depth of prey capture events during each foraging trip, and the mean distance of prey captures from the colony during each foraging trip, and assessed how these varied intra- and inter-annually in relation to offshore SST (described previously).We assessed the spatial distribution of prey capture events in relation to SST. We performed a linear interpolation between GPS locations at 1 s intervals to integrate the accelerometry record and the GPS tracks. When a location was determined for each prey capture event, we used only these locations in the analysis. We used the same 1 kmAll analyses conducted in this study were performed in the R statistical programming frameworkThe Macquarie University Animal Ethics Committee approved all animal research protocols, which were undertaken in accordance with guidelines set out by Australian law .Penetration of the East Australian Current was variable over the three study years . In 2012We obtained accelerometry profiles for 63 penguin foraging trips between Nov 2012 and Dec 2014 . The mean number of prey caught per 90 minute period varied both intra- and inter-annually see   showed a broad correlation with prey capture success as determined by both 90-minute prey capture and CPUE metrics. 2012 was the year with lowest SSTs , and saw the highest foraging success. 2013 was anomalously warm,  and saw the lowest foraging success. 2014 was intermediate in both SST and foraging success (Nov = +0.09 °C and Dec = +0.07 °C). In September this trend was reversed with 2013 being warmer with higher prey capture success, although there was low variability in SST between the two years .2 = 0.31, F = 5.79, p = 0.0002). There was no strong relationship between CPUE and SST between 16 °C and 19 °C, when again the model showed a strong peak in CPUE around 20 °C before a drop off between 21 °C and 22 °C .Offshore SST had a quadratic relationship with both log transformed prey captures per 90 min and CPUE . For the2 grid cells that penguins could have visited during single day trips did not contain observations of penguins, indicating that penguins were selective in their habitat choice, foraging in similar locations within a given time period.For the habitat use analysis, we analysed GPS tracks from a total of 112 single day penguin foraging trips in September, November and December 2012–14 . 82% of 1 kmPenguins appeared to seek out water that was colder than the mean of all available habitat . When a The hurdle model using SST averaged over the sampling days as a predictor performed better than models using SST anomaly either as a continuous or binary variable see . The cou2 grid cell at the coldest and warmest temperatures observed during this study .To assess the effect of SST on the spatial distribution of prey captures, we integrated accelerometry profiles and GPS tracks of 50 complete single day penguin foraging trips in November and December 2012–14, and September 2013–14 . Sample penguin tracks with prey capture locations in relation to gridded SST are shown in is study . The GAMThe GAM only assessed the effect of SST on prey capture success in areas where prey capture occurred. To assess the relationship between prey capture and the SSTs encountered over the course of a foraging trip, we plotted a time-series of the mean SST of grid cells visited by penguins in 10% increments of trips within a sampling period . We then overlaid the mean number of prey captures identified using accelerometry within the same 10% increments within a sampling period  see .This analysis confirmed that penguins seek out areas with lower relative SSTs, with encountered temperatures always decreasing during a foraging trip before increasing again towards the end of a journey. It also showed that in December 2012–14 and November 2012 and 2014, there was good agreement between the spatial distribution of prey capture success and SST, with areas/periods of lowest SST encountered by penguins on a foraging trip related to the highest prey capture success. However, in September 2013–14 and November 2013 there was no clear relationship between spatial prey capture and SST distribution.2 grid cell and the mean temperature at the point of prey capture in the same grid cell, calculated from the temperature sensors on board the accelerometers. We found a near linear, 1:1 relationship between SST and prey capture temperature above 16 °C   . This is 0.0001) .2 = 0.46, F = 9.602, P < 0.0001) . It appears that prey captures occurred further from the colony when SST was relatively warm . This wa 0.0001) .Southeast Australia is a hotspot for ocean warming driven by the EAC, with SST rises of 0.7–1.4 °C predicted by 2030, and 2–3 °C by 2100Little penguins feed on a variety of low trophic level species, with “forage fish” e.g. small pelagic fish, squid and krill comprising most of their diet throughout their range29Although we only studied prey capture by penguins over three breeding seasons, SST during the study period varied substantially around the long-term mean, situating our findings within a climatological context. This was due to variable dynamics of the EAC, with unusual spikes of warm water penetrating the region in the spring and summer of 2013 and 2014. We found that a simple but reliable predictor of relative foraging success in November and December was whether SST was high or low relative to the same month in the other study years, with the year with the lowest mean temperatures (2012) having the highest success and the year with the highest mean temperatures (2013) having the lowest .A broad correlation between anomalously high SST and the availability of forage fish is seen in other western boundary current systems. In the Sea of Japan, which is influenced by the warm Kuroshio Current, sardine catches are lowest when SST is higha concentrations by around 150%. This bloom is driven by a seasonal increase in SST, greater availability of dissolved nitrate and silicate, and a shallowing of the mixed-layer depth: conditions that promote rapid phytoplankton growth and reproductionAlthough high SST was inversely related to foraging success on a monthly scale, our modelled data showed that the functional relationship between prey capture success and SST was not linear. At the lowest SSTs, prey capture success was also low. At latitudes around Montague Island (~ −36.5 S), a major phytoplankton bloom occurs each spring that increases local chlorophyll  °C, with lower success outside that range (Sardinops sagax) catches and SST in the Gulf of California, South Africa and South Australia324445Our models suggest an optimal offshore temperature range for prey capture success of 19–21at range . AlthougOur results imply that offshore SST > 21 °C is related to lower prey capture success by penguins breeding on Montague Island. In an average year, these temperatures are not experienced until January, the tail end of the little penguin’s breeding season. However, in anomalous years such as 2013, pulses of warm water arrive earlier and coincide with the peak chick-provisioning period, a time of high energetic demand49515254It is apparent from overlaying tracks on SST anomaly maps and from the hurdle model results that little penguin foraging tends to be focused in habitat with lower SST . Little 56We found a relationship between prey capture success and SST that was not accounted for by habitat preference. Even within the cooler areas that penguins selected for foraging, and in those areas that actually contained prey, the amount of prey caught was related to SST. The coldest areas provided the highest prey capture success, and the warmest areas provided the lowest prey capture success, indicating that prey distribution may be responsive to fine-scale SST. An inverse relationship between local forage fish distribution and SST has also been observed in eastern South Africa, where sardines appear to be spatially aggregated in the coolest available habitat, pushed inshore to small patches of suitable habitat by shoreward movement of the warm Agulhas currenthttp://www.marine.csiro.au/~dunn/cars2009/) and there was no evidence of a thermocline from the tag temperature data at the depths at which penguins were catching prey, it seems that whichever prey species the penguins were primarily feeding on during this period were not consistently aggregated around such subsurface features that may be related to EAC dynamics.The penguins in this study appeared to consistently forage near the surface (<10 m). This suggests that the distribution of the prey species that they were targeting was similar throughout the study period, and that the penguins maintain a relatively consistent foraging strategy, even though prey capture success can be highly variable. In previous studies of little penguinsin situ environmental data. This will shed light on the types and densities of prey in the area at different times, and their fine-scale distribution in relation to the environment. Tracking studies of breeding seabirds could assess the ‘energy landscape’ in the region by estimating spatial gradients of energy expenditureOur results suggest a relationship between the distance from the colony at which penguins catch most of their prey and offshore SST, with the highest SSTs being associated with the furthest foraging distances. This was influenced by penguins travelling unusually far in December 2013 and 2014, when SST was comparatively high. Increases in foraging effort (e.g. distance travelled and dive behaviour) in response to shifts in the location of profitable feeding areas may ultimately affect population dynamicsMarine predator populations are vulnerable to reductions in prey availability49323840How to cite this article: Carroll, G. et al. High sea surface temperatures driven by a strengthening current reduce foraging success by penguins. Sci. Rep. 6, 22236; doi: 10.1038/srep22236 (2016).


The estimated 1 million deaths/year where bone metastasis is present, and the high healthcare costs required for its management, have ignited intensive research into the cellular and molecular pathology of osteolysis, involving interplay between tumour cells, bone‐forming osteoblasts and bone‐degrading osteoclasts. Compared to bone metastasis, knowledge about the pathology of primary bone cancers is limited. In recent work published in this journal, Engelholm et al provide a unique insight into how this poorly understood disease manifests and destroys bone. For the first time they have demonstrated that a mouse monoclonal antibody targeting the collagen receptor Endo180  can prevent osteolysis and bone destruction in a syngeneic model of advanced osteosarcoma. Their convincing findings make an important contribution towards Endo180‐based therapy being developed as an option for the treatment of bone cancer amongst other malignancies. © 2015 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.Skeletal bone is an attractive site for secondary tumour growth and is also home to spontaneous primary cancer. Treatment of bone metastasis is focused on limiting the vicious cycle of bone destruction with bisphosphonates or inhibition of receptor activator of nuclear factor‐ This syngeneic mouse model recapitulated the observations made in human specimens, with abundant layers of Endo180/MT1‐MMP‐positive NCTC‐2472 cells sitting on bone surfaces that were virtually devoid of osteoclasts. Treatment with the monoclonal antibody (mAb) 5f4, which recognizes an epitope in the first three N‐terminal domains of Endo180 [cysteine‐rich domain (CRD), FNII and the first C‐type lectin domain (CTLD) out of eight, CTLD1  of Endo180 et alIn accordance with the findings of Engelholm et al pinpoints the malignant cells in the tumour mass as the major participants in osteolysis in vitro model to recapitulate the bone‐forming side of this complex setting, Endo180 was identified as a modulator of mineralized type I collagen deposition in primary human osteoblasts that is activated by the transforming growth factor‐β1 (TGFβ1) and TGFβ1 receptor (TGFβ1R) signalling axis and suppressed by paracrine signals from adjacent tumour cells The mechanism of tumour‐mediated bone degradation proposed by Engelholm et al, cathepsin K expression has been demonstrated in osteoblasts and tumour cells associated with osteosarcoma, giant cell tumour of bone and prostate cancer Osteolysis mediated by osteoclasts requires the formation of sealing zones on the bone surface and the localized release of cathepsin K, which is the only enzyme capable of degrading the mineralized type I collagen matrix of bone. In support of the model proposed by Engelholm Endo180‐dependent chemotaxis towards collagen fragments or urokinase plasminogen activator (uPA) is linked respectively to osteoblast recruitment to sites of bone degradation under normal physiological conditions et alIn a snapshot, the advances that have been made since Endo180 was first isolated 25 years ago have led us towards the exciting findings of Engelholm