Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution.

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form

Effect of Gamma Irradiation on the Physico-chemical Characterstics of Groundnut (Arachis Hypogaea)

Abs tract: The aim of this st u d y wa s to evaluate the effect of gamma irradiation on phys ico-chemical properties of groundnut as well as to in v e s t igate its impact on quality attributes of groundnut oil. S e eds of two cultivars of ground nut (Arachis hypogaea) namely Sodari and Madani we re g a mmairradiated at dos e levels of 1, 1.5 and 2 kGys . Proximate compos ition, a s h min e ra ls , iodine value, acid value, peroxide value, s aponification value, oil refractive ind e x, oil relative vis cos ity, in-vitro protein diges tibility, nitrogen s olubility, water holding capacity, oil holding capacit y , b u lk d ens ity, emuls ion activity, emuls ion capacity, e mu ls io n s tability, foam capacity and foam s tability were determined for raw and irra d ia t e d s eeds . The res ults revealed that the effect of gamma irradiation on protein, oil, fiber, carbohydrates and minerals content of grou n d nut seeds was of no cons is tent pattern, however, for the quality attributes of groundnut oil, g amma irradiation caus ed significant d e c re ase (P# 0.05) in iodine value and s ignificant increas e in acid and peroxide values for b o t h cultivars , with exception of the acid value of Madani cultivar. W hile saponification value, refractive index and viscos ity of grou n dnut oil for both cultivars were not affected significantly by gamma irradiation. Moreo v e r, a s c ompared with untreated groundnut flour, for both cultivars , water holding c a pacity, bulk density, emuls ion activity and emuls ion capacity of groundnut flour were n o t s ignificantly affected by gamma irradiation. On the other hand, foaming s tability wa s a ffe c t e d negatively with gamma irradiation. Generally, s light differences between the two cultivars s tudied were obs erved for the different properties tes ted

PRMT5 protects genomic integrity during global DNA demethylation in primordial germ cells and preimplantation embryos.

Primordial germ cells (PGCs) and preimplantation embryos undergo epigenetic reprogramming, which includes comprehensive DNA demethylation. We found that PRMT5, an arginine methyltransferase, translocates from the cytoplasm to the nucleus during this process. Here we show that conditional loss of PRMT5 in early PGCs causes complete male and female sterility, preceded by the upregulation of LINE1 and IAP transposons as well as activation of a DNA damage response. Similarly, loss of maternal-zygotic PRMT5 also leads to IAP upregulation. PRMT5 is necessary for the repressive H2A/H4R3me2s chromatin modification on LINE1 and IAP transposons in PGCs, directly implicating this modification in transposon silencing during DNA hypomethylation. PRMT5 translocates back to the cytoplasm subsequently, to participate in the previously described PIWI-interacting RNA (piRNA) pathway that promotes transposon silencing via de novo DNA remethylation. Thus, PRMT5 is directly involved in genome defense during preimplantation development and in PGCs at the time of global DNA demethylation.U.G. was supported by a Marie Sk1odowska Curie Intra-European Fellowship. J.J.Z. was a recipient of a Wellcome Trust PhD Studentship (RG44593). This research was supported by grants from the Wellcome Trust to M.A.S. (WT096738).This is the final published version. It first appeared at http://www.cell.com/molecular-cell/abstract/S1097-2765%2814%2900787-4

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form

Incarceration history and risk of HIV and hepatitis C virus acquisition among people who inject drugs: a systematic review and meta-analysis

Background People who inject drugs (PWID) experience a high prevalence of incarceration and might be at high risk of HIV and hepatitis C virus (HCV) infection during or after incarceration. We aimed to assess whether incarceration history elevates HIV or HCV acquisition risk among PWID. Methods In this systematic review and meta-analysis, we searched MEDLINE, Embase, and PsycINFO databases for studies in any language published from Jan 1, 2000 until June 13, 2017 assessing HIV or HCV incidence among PWID. We included studies that measured HIV or HCV incidence among community-recruited PWID. We included only studies reporting original results and excluded studies that evaluated incident infections by self-report. We contacted authors of cohort studies that met the inclusion or exclusion criteria, but that did not report on the outcomes of interest, to request data. We extracted and pooled data from the included studies using random-effects meta-analyses to quantify the associations between recent (past 3, 6, or 12 months or since last follow-up) or past incarceration and HIV or HCV acquisition (primary infection or reinfection) risk among PWID. We assessed the risk of bias of included studies using the Newcastle-Ottawa Scale. Between-study heterogeneity was evaluated using the I2 statistic and the P-value for heterogeneity. Findings We included published results from 20 studies and unpublished results from 21 studies. These studies originated from Australasia, western and eastern Europe, North and Latin America, and east and southeast Asia. Recent incarceration was associated with an 81% (relative risk [RR] 1·81, 95% CI 1·40–2·34) increase in HIV acquisition risk, with moderate heterogeneity between studies (I2=63·5%; p=0·001), and a 62% (RR 1·62, 95% CI 1·28–2·05) increase in HCV acquisition risk, also with moderate heterogeneity between studies (I2=57·3%; p=0·002). Past incarceration was associated with a 25% increase in HIV (RR 1·25, 95% CI 0·94–1·65) and a 21% increase in HCV (1·21, 1·02–1·43) acquisition risk. Interpretation Incarceration is associated with substantial short-term increases in HIV and HCV acquisition risk among PWID and could be a significant driver of HCV and HIV transmission among PWID. These findings support the need for developing novel interventions to minimise the risk of HCV and HIV acquisition, including addressing structural risks associated with drug laws and excessive incarceration of PWID

Origin and segregation of the human germline

Acknowledgements This work was supported by the Wellcome Investigator Awards in Science (2094)75/Z/17/Z (to MA Surani), the Wellcome Investigator Awards in Science 096738/Z/11/Z (to MA Surani), the BBSRC research grant G103986 (to MA Surani), the Croucher Postdoctoral Research Fellowship (to WWC Tang), the Wellcome 4-Yr PhD Programme in Stem Cell Biology & Medicine (2038)31/Z/16/Z (to A Castillo-Venzor) and the Cambridge Commonwealth European and International Trust (to A Castillo-Venzor), the Isaac Newton Trust (to WWC Tang), the Butterfield Awards of Great Britain Sasakawa Foundation (to T Kobayashi and MA Surani), and the Astellas Foundation for Research on Metabolic Disorders (to T Kobayashi). The marmoset embryo research is generously supported by the Wellcome Trust (WT RG89228, WT RG9242), the Centre for Trophoblast Research, the Isaac Newton Trust, and JSPS KAKENHI 15H02360, 19H05759. TE Boroviak was supported by a Wellcome Sir Henry Dale Fellowship. JC Marioni acknowledges core support from EMBL and from Cancer Research UK (C9545/A29580), which supports MD Morgan. We would like to thank Roger Barker and Xiaoling He for providing human embryonic tissues and Charles Bradshaw for bioinformatics support. We also thank The Weizmann Institute of Science for the WIS2 human PSC line and the Genomics Core Facility of CRUK Cambridge Institute for sequencing services. We thank members of the Surani laboratory for insightful comments and critical reading of the manuscript.Peer reviewedPublisher PD

A PAX5-OCT4-PRDM1 developmental switch specifies human primordial germ cells.

Dysregulation of genetic pathways during human germ cell development leads to infertility. Here, we analysed bona fide human primordial germ cells (hPGCs) to probe the developmental genetics of human germ cell specification and differentiation. We examined the distribution of OCT4 occupancy in hPGCs relative to human embryonic stem cells (hESCs). We demonstrated that development, from pluripotent stem cells to germ cells, is driven by switching partners with OCT4 from SOX2 to PAX5 and PRDM1. Gain- and loss-of-function studies revealed that PAX5 encodes a critical regulator of hPGC development. Moreover, an epistasis analysis indicated that PAX5 acts upstream of OCT4 and PRDM1. The PAX5-OCT4-PRDM1 proteins form a core transcriptional network that activates germline and represses somatic programmes during human germ cell differentiation. These findings illustrate the power of combined genome editing, cell differentiation and engraftment for probing human developmental genetics that have historically been difficult to study

Remembering Our Past: Teaching the History of Anatomy at Indiana University

Most students pursuing careers in anatomy or related disciplines have a limited understanding of how, over the centuries, the intricate structure of the human body came to be known. To provide students with the relevant historical perspective, we developed a team-taught survey course in the history of anatomical sciences—including gross anatomy, histology, neuroanatomy, and embryology—from antiquity to the present. Taught entirely via Zoom during the Spring semester of 2021, History of Anatomy (2 semester hours credit) met once per week for approximately 2 hours. Enrollment consisted of 5 undergraduate students majoring in Biology (2), Human Biology (2), or Anthropology (1), as well as 3 graduate students pursuing either a master’s degree in Clinical Anatomy (1) or a Ph.D. in Anatomy Education (2). Three of the students had no prior coursework in anatomy. Through assigned readings, lectures, and discussions, the class explored the work of the great anatomists and their discoveries. A particular emphasis was placed on the evolution of anatomy as a discipline and the cultural influences, scientific controversies, and ethical dilemmas facing its practitioners. Syllabus topics included critical appraisals of the role of gender, race, and ethnicity in anatomical discovery. A key feature of the course was the opportunity for students to engage in robust discussions about such controversial issues as: Eurocentric biases in our understanding of human anatomy and the untold story of Muslim contributions to anatomical knowledge well before Vesalius; Competing claims of priority for who “discovered” the pulmonary circulation; The underappreciated role of women in the history of anatomy and medicine; The ethical quandary of teaching anatomy from archival fetal specimens obtained before the era of informed consent; Accusations that famed anatomist William Hunter used the bodies of murdered pregnant women to create his anatomical atlas of the gravid uterus; Complicity of Eduard Pernkopf and other Nazi-era anatomists in the unethical use of executed victims to obtain images for a renowned anatomical atlas. All students were assessed through weekly homework (written responses to study questions), a mid-term writing assignment, and a term paper about an historical topic of the student’s choosing. Graduate students had the additional requirement of a class presentation about their term paper topic. The end-of-course evaluation suggested that the course was well-received by the students (mean Likert score = 4.63 on a 5-point scale; n = 6). Based on this positive reception, we plan to offer History of Anatomy again on a recurring basis. We believe that by knowing our history, both the good and the bad, future practitioners of anatomy and related disciplines will be less likely to perpetuate the biases and ethical transgressions of earlier eras.American Association for Anatomy Spring Meetin

An assessment of vulnerability to HIV infection of boatmen in Teknaf, Bangladesh

<p>Abstract</p> <p>Background</p> <p>Mobile population groups are at high risk for contracting HIV infection. Many factors contribute to this risk including high prevalence of risky behavior and increased risk of violence due to conflict and war. The Naf River serves as the primary border crossing point between Teknaf, Bangladesh and Mynamar [Burma] for both official and unofficial travel of people and goods. Little is known about the risk behavior of boatmen who travel back and forth between Teknaf and Myanmar. However, we hypothesize that boatmen may act as a bridging population for HIV/AIDS between the high-prevalence country of Myanmar and the low-prevalence country of Bangladesh.</p> <p>Methods</p> <p>Methods included initial rapport building with community members, mapping of boatmen communities, and in-depth qualitative interviews with key informants and members from other vulnerable groups such as spouses of boatmen, commercial female sex workers, and injecting drug users. Information from the first three stages was used to create a cross-sectional survey that was administered to 433 boatmen.</p> <p>Results</p> <p>Over 40% of the boatmen had visited Myanmar during the course of their work. 17% of these boatmen had sex with CSW while abroad. There was a significant correlation found between the number of nights spent in Myanmar and sex with commercial sex workers.</p> <p>In the past year, 19% of all boatmen surveyed had sex with another man. 14% of boatmen had participated in group sex, with groups ranging in size from three to fourteen people. Condom use was rare {0 to 4.7% during the last month}, irrespective of types of sex partners. Regression analysis showed that boatmen who were 25 years and older were statistically less likely to have sexual intercourse with non- marital female partners in the last year compared to the boatmen aged less than 25 years. Similarly deep-sea fishing boatmen and non-fishing boatmen were statistically less likely to have sexual intercourse with non- marital female partners in the last year compared to the day long fishing boatmen adjusting for all other variables. Boatmen's knowledge regarding HIV transmission and personal risk perception for contracting HIV was low.</p> <p>Conclusion</p> <p>Boatmen in Teknaf are an integral part of a high-risk sexual behaviour network between Myanmar and Bangladesh. They are at risk of obtaining HIV infection due to cross border mobility and unsafe sexual practices. There is an urgent need for designing interventions targeting boatmen in Teknaf to combat an impending epidemic of HIV among this group. They could be included in the serological surveillance as a vulnerable group. Interventions need to address issues on both sides of the border, other vulnerable groups, and refugees. Strong political will and cross border collaboration is mandatory for such interventions.</p