Identification of 5′-deoxyribose phosphate lyase activity in human DNA polymerase γ and its role in mitochondrial base excision repair in vitro

Mitochondria have been proposed to possess base excision repair processes to correct oxidative damage to the mitochondrial genome. As the only DNA polymerase (pol) present in mitochondria, pol γ is necessarily implicated in such processes. Therefore, we tested the ability of the catalytic subunit of human pol γ to participate in uracil-provoked base excision repair reconstituted in vitro with purified components. Subsequent to actions of uracil-DNA glycosylase and apurinic/apyrimidinic endonuclease, human pol γ was able to fill a single nucleotide gap in the presence of a 5′ terminal deoxyribose phosphate (dRP) flap. We report here that the catalytic subunit of human pol γ catalyzes release of the dRP residue from incised apurinic/apyrimidinic sites to produce a substrate for DNA ligase. The heat sensitivity of this activity suggests the dRP lyase function requires a three-dimensional protein structure. The dRP lyase activity does not require divalent metal ions, and the ability to trap covalent enzyme-DNA complexes with NaBH4 strongly implicates a Schiff base intermediate in a β-elimination reaction mechanism.

Links between replication and recombination in Saccharomyces cerevisiae: A hypersensitive requirement for homologous recombination in the absence of Rad27 activity

The RAD27 gene of Saccharomyces cerevisiae encodes a 5′-3′ flap exo/endonuclease, which plays an important role during DNA replication for Okazaki fragment maturation. Genetic studies have shown that RAD27 is not essential for growth, although rad27Δ mutants are temperature sensitive. Moreover, they exhibit increased sensitivity to alkylating agents, enhanced spontaneous recombination, and repetitive DNA instability. The conditional lethality conferred by the rad27Δ mutation indicates that other nuclease(s) can compensate for the absence of Rad27. Indeed, biochemical and genetical analyses indicate that Okazaki fragment processing can be assured by other enzymatic activities or by alternative pathways such as homologous recombination. Here we present the results of a screen that makes use of a synthetic lethality assay to identify functions required for the survival of rad27Δ strains. Altogether, we confirm that all genes of the Rad52 recombinational repair pathway are required for the survival of rad27Δ strains at both permissive (23°C) and semipermissive (30°C) temperatures for growth. We also find that several point mutations that confer weaker phenotypes in mitotic than in meiotic cells (rad50S, mre11s) and additional gene deletions (com1/sae2, srs2) exhibit synthetic lethality with rad27Δ and that rad59Δ exhibits synergistic effects with rad27Δ. This and previous studies indicate that homologous recombination is the primary, but not only, pathway that functions to bypass the replication defects that arise in the absence of the Rad27 protein.

Platelet-derived growth factor BB induces functional vascular anastomoses in vivo.

Neovascularization that generates collateral blood flow can limit the extent of tissue damage after acute ischemia caused by occlusion of the primary blood supply. The neovascular response stimulated by the BB homodimeric form of recombinant platelet-derived growth factor (PDGF-BB) was evaluated for its capacity to protect tissue from necrosis in a rat skin flap model of acutely induced ischemia. Complete survival of the tissue ensued, when the original nutritive blood supply was occluded, as early as 5 days after local PDGF-BB application, and the presence of a patent vasculature was evident compared to control flaps. To further evaluate the vascular regenerative response, PDGF-BB was injected into the muscle/connective tissue bed between the separated ends of a divided femoral artery in rats. A patent new vessel that functionally reconnected the ends of the divided artery within the original 3- to 4-mm gap was regenerated 3 weeks later in all PDGF-BB-treated limbs. In contrast, none of the paired control limbs, which received vehicle with an inactive variant of PDGF-BB, had vessel regrowth (P < 0.001). The absence of a sustained inflammatory response and granulation tissue suggests locally delivered PDGF-BB may directly stimulate the angiogenic phenotype in endothelial cells. These findings indicate that PDGF-BB can generate functional new blood vessels and nonsurgically anastomose severed vessels in vivo. This study supports the possibility of a therapeutic modality for the salvage of ischemic tissue through exogenous cytokine-induced vascular reconnection.

Hādhā kitāb Kurūm ʻarāyis al-tahānī sharḥ Ṣalawāt Ibn Mashīsh al-Dānī / taʼlīf al-Imām al-Fāḍil al-Ṣūfī al-Humām al-Shaykh Muṣṭafá al-Bakrī al-Ṣiddīqī al-Khalwatī : manuscript, 1840

Author's own abridgement of his longer commentary on Moroccan sufi Ibn Mashīsh's prayer book known as Ṣalawāt. Longer version is titled: Rawḍāt al-ʻarshīyah fī al-kalām ʻala al-Ṣalawāt al-Mashīshīyah.

Hādhā kitāb Ḥusn al-muḥāḍarah fī akhbār Miṣr wa-al-Qāhirah / lil-Imām al-Mujtahid al-Ḥafīẓ Jalāl al-Dīn ʻAbd al-Raḥmān al-Asyūṭī : manuscript, 1844

Vol. 1 of a multi-volume set.

Kitāb Laṭāʼif akhbār al-uwal fī-man taṣarrafa fī Miṣr min al-duwal / taʼlīf sayyidinā wa-mawlānā al-ʻālim al-ʻallāmah Muḥammad ibn ʻAbd al-Muʻṭī ibn Abī al-Fatḥ ibn Aḥmad ibn ʻAbd al-Ghanī ibn ʻAlī al-Isḥāqī al-Shāfiʻī : manuscript, 1733

بسم الله الرحمن الرحيم فهو حبي اكفي الحمد لله الملك العزيز في ملكه واقتذاره الذي ملك الوجود يقوته واوجد بارادته واختياره... :Incipit

Kitāb al-Uns wa-al-īnās fī futūḥ Ifrīqīyah ilá madīnat Fās : manuscript, 1795

الحمد لله مانح النعم فضلا من عنده المحسن بما يقوم به احدا بحقه وان بالغ غاية جهده... :Incipit

Kitāb al-Jaʻrāfīyah : manuscript, undated

Probably Zuhrī's third edition of the "al-Ṣūrah al-Maʼmūnīya" (al-Maʼmūn's "Mappa Mundi").

Maqāmāt : manuscript, undated

بسم الله الرحمن الرحيم اللهم انا نحمدك على ما علمت في البيان والهمت في البيان كما نحمدك على ما مبعت في الغطا... :Incipit

Mihr va Mushtarī : manuscript, undated

According to a note in a later hand on fly leaf 1, poem composed in 1376 AD.

Dekâiku'l-hakâik : manuscript, undated

A work on subtleties of Persian vocabulary. Discusses nuances of and differences in meaning between homographs or near-homographs and words derived from similar stems. Pronunciations, etymologies, differences in usage discussed. Poems used as examples.

Menâkıb-ı Mevlânâ : manuscript, [1827]

Legends about Jalāladdīn Rūmī. One lengthy story narrates a conversation the author had with Rūmī in his dream.

Sharḥ al-Nukhbah fī uṣūl ʻilm al-ḥadīth / lil-ʻAllāmah Ibn Ḥajar : manuscript, 1725 or 1726

Title from f. 1r.

Itḥāf al-dhakī bi-sharḥ al-Tuḥfah al-mursalah ilá al-Nabī : manuscript, [ca. 1670]

Title from ff. 1r and f. 2r.

Hādhihi risālat al-ʻIqd al-thamīn fī sharḥ al-ḥadīth al-musalsal bi-al-Dimashqīyīn / taʼlīf al-Shaykh al-Imām al-ʻĀlim al-ʻĀmil al-Shaykh Ismāʻīl al-ʻAjlūnī : manuscript, [1749 or 1750]

Ownership statements on f. 1r signed ʻAlī al-ʻImādī, 1175 AH [1761 or 62 AD]; Ḥāmid al-Bakrī, 1192 AH [1178-9 AD]; Muḥammad ibn Saʻīd ibn Amīn al-Munayyir (or: al-Munīr), Jumādá al-Thānī 1243 [1827-8]. On fly leaf [1]: Muḥammad Saʻīd ... al-Ḥusaynī al-Dimashqī, Rabīʻ al-Awwal [1]282 [1865]; Muḥammad Abū al-... al-Ḥusaynī al-..., 17 Jumādá al-ūlá 1317 [1899];.