|Nature||A new small-bodied hominin from the Late Pleistocene of Flores, Indonesia||P. Brown et al.||Oct 28 2004||431||1055-1061||Paola|
|A new dwarfed species of hominid was recently discovered in the Island of Flores, Indonesia. The hominin was only 1 meter tall, with a brain of about one third of the modern human's brain size. Researchers found an extremely well conserved female skeleton and bones and teeth from at least other 7 individuals. Bones of komodo dragons and the pigmy elephant Stegodon were also found nearby. Preliminary dating places Flores about 18,000 years ago and suggests that Flores might be the descendent of Homo erectus, previously discovered in nearby Island of Java. Researchers are now hoping to find DNA in the bones to clarify the relationship of Flores with the other species. Certainly, the samll size of this new dwarfed species suggests that humans are subject to the same evolutionary forces that made other mammals shrink to dwarf size when in genetic isolation or under evolutionary pressure.|
|Nature||'Structure of a Glutamate Transporter Homologue from Pyrococcus horikoshii"||Yernool, D., Boudker, O., & Gouaux, E.||14 Oct. 2004||431||811-818||Scott|
|Yernool et al. have completed a 3.5-Angstom structure of an archaeal homolog of the eukaryotic glutamate transporter family (37% sequence identity with human excitatory amino acid transporter 2 -- hEAAT2). This is a remarkable (and very novel) membrane protein each subunit of which has 8 transmembrane helices (4 with have significant irregularities) and two helix-turn-helix "paddles" that function in a proposed, plausible glu-transport mechanism. The trimeric structure generates a striking 50-Angstrom-diameter, 30-Angstrom-deep basin or cavity that faces the extracellular milieu and has 3 substrate binding sites near the bottom. Thus the glu diffuses to a binding site that is already half-way across the membrane. The authors have a fairly convincing argument in support of their version of Jardetzky's (1966) "alternating access mechanism" for cross-membrane transport. Given the immense importance of glu transport in the nervous system, this structure will doubtless stimulate a great deal of new research, not least of all on the sites and roles of the cotransported (3Na+ and 1H+ per glu) and antitransported (1K+ per glu) as well as the glutamate-gated Cl- transport that proceeds independently. Look for (likely) forthcoming structures that can define the different conformational states involved in the mechanism.|
|Nature||Who said 'helix'?||W. Fuller||21 Aug 2003||424||876-878||Kavitha|
|An interesting read about the history of the discovery of the DNA double helix and an attempt to provide an accurate perspective
about the much debated role of Maurice Wilkin (vs. that of Rosalind Franklin). The author makes references to various communications
from which the complex interactions between their two laboratories, and with Watson/Crick is evident. The scientific attitude of not
only Franklin, but also the King's College labs as a whole apparently led to Franklin unfortunately working in isolation. Perhaps
Wilkins' attitude of sharing data more freely, combined with the significant body of work he produced before and after Franklin's
crucial contribution, merited his inclusion in the Nobel. In a subsequent letter to the editor in Nature, Sept 4, 2003 (pg 15),
D. Zallen (Virginia Tech) quotes a letter from Crick that clearly recognizes the effort of Franklin ("the data which really helped
us obtain the structure was mainly obtained by Rosalind Franklin") but gives more credit to Wilkins for initiating the X-ray work
and for strongly favouring the helical hypothesis.
|Structure||The Structure of the Extracellular Region of Human Hepsin Reveals a Serine Protease Domain and a Novel Scavenger Receptor Cysteine-Rich (SRCR) Domain||Somoza et al.||September 2003||11||1123||Masashi|
|Hepsin is an integral membrane protein and correlates with some types of cancer.
In this article, the author reports crystal structure of extracellular component of human hepsin. This structure is comprised of two domains, namely, a trypsin-like serine protease
domain and a novel member of SRCR domains.
These two domains are covalently bound to each other through a single disulfide bond instead of a peptide bond. The cysteine residue on the protease domain is conserved in
many serine proteases and anchors various accessory domains.
|Science||Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization||Riesebers, Raymond, Rosenthal, Lai, livingstone, Nakazato, Durphy, Schwarzbach, Donovan, Lexer||29 Aug 2003||301||1211-1216||Paola|
|This article by Rieseberg et al. explores the role of hybridization in evolution. The sunflower hybrids under study have derived independently from two species and occupy habitats highly different from those of their parents. The results of the study show that hybridization plays a key role in evolution as long as there is adaptation. In fact, in order to survive, the interspecific hybrids must escape the "minority disadvantage" . This is achieved by a simple mechanism such as discrete and divergent ecological niche colonization. Unlike mutation, this mechanism provides a rapid and large genetic variation in thousands of genes in a sigle generation. Also,
the study shows that morphological and ecological differences between the hybrid sunflower species can be recreated through contemporary hybridization.
|Science||Sex, sunflowers, and speciation||R.J. Abbott||29 Aug 2003||301||1189-1190||Paola|
|This article by R. Abbott provides a simple and clear background about how interspecific hybridization occurs and how it affects the evolution of new species.
Hybridizatioon between different species of plants is prevented by both prezygotic(specific pollinators, specific habitat, spatial isolation) and postzygotic barriers (mating of a fertile hybrid with a parent results in sterile offspring or no offspring). Due to "leakage" in the prezygotic barriers, some interspecific hybrids may result. Strong postzygotic barriers prevent the hybrid from mating with parents and therefore the hybrid exhibits low fertility since it represents a minority in a parent population. However, the "minority type disadvantage" can be overcome if the hybrid adapts to different habitats where it is isolated from both parents. Thus, the hybrid can establish as new specie.
|Science||The Protein Kinase Complement of the Human Genome||G. Manning, D.B. Whyte, R. Martinez, T. Hunter, S. Sudarsanam||Dec 6, 2002||Volume 298 Number 5600||1912-1934||Esther|
|This article recommended by Temple.|
|Science||Crystal Structure of the Extracellular Segment of Integrin aVb3||Xiong et al.||Oct 12, 2001||294||339-345||Hongxian|
|Integrins are large, heterodimeric (alpha/beta) transmembrane proteins that bind to many extracellular
components. In this article, the author reports the crystal structure of the extracellular regions of the
complex aV and b3. Among the 12 domains, the most interesting are the N-terminal beta-propellar domain
from the alpha chain and the A domain from the beta chain. The interface between these two domains remarkably
resembles the one between the alpha and beta subunits of the G proteins. Unlike the G protein beta subunit,
which is a 7 WD repeats containing protein, this beta-propellar domain does not to belong to this ancient
family (BMERC WD Repeat Proteins ).
|science||Global Analysis of Protein Activities Using Proteome Chips||Michael Snyder||Sept. 14, 2001||293||2101-2105||Shengsheng|
|An interesting paper. These researchers constructed a yeast proteome (well, strictly speaking, ~80% of the yeast proteins ) microarray and performed protein activity assays on it. The protein activities
include interaction with calmodulin and phospholipid. My concern is: as the expressed proteins were fused proteins with 6-histidine tag still on them, to make sure all these proteins fold properly for a successful protein-protein
interaction analysis would be a great challenge.
|Science||New Leads on the 'How' of Alzheimer's||Sep 21 ||293||Shengsheng|
|After almost a hundred years' study of Alzheimer's disease, the cause of AD is still a mystery.
This article (in the section of News Focus-NEUROSCIENCE) summarized
researches in recent years that support one of the theories: apoptosis is the culpritof AD (of course with great controversy, like all other theories). A nice diagram shows routes
to apoptosis (shouldn't it be "possible" routes?) and describes the process of caspase
activation that leads to apoptosis. Pay attention to "?" in this diagram, I believe the apoptosis supporters would have a hard time to explain these question marks,
like how APP is cleaved by caspases (don't forget APP is a transmembrane protein) to produce Abeta.
|Science||he Mitochondrion: Is It Central to Apoptosis?||Finkel, E||Apr 27, 20001||292||624-626||Hongxian|
|The debate is still ongoing as whether mitochondria are primary in triggering programmed cell death, or the primary apoptosis signals
route directly to caspases without first involving the mitochondria. The debate is hard to resolve because the events of apoptosis
unfold too rapidly to determine their temporal sequence, and the use of techniques such as knocking out the genes for various components
of the apoptosis pathways has be inconclusive.
|Science||A Sperm Cytoskeletal Protein That Signals Oocyte Meiotic Maturation and Ovulation||MA Miller, et al.||Mar 16, 2001||291||2144-2147||Hongxian|
|A well-known protein in nematode sperm, the major sperm cytoskeletal protein (MAP), turns out to be
a bipartite signaling molecule that can both induce oocytes to mature and stimulate ovulation by
causing gonad sheath cells to contract. This protein thus defines an entirely new class of extracellular
|Science||Requirement of the RNA Editing Deaminase ADAR1 Gene for Embryonic Erythropoiesis ||Q. Wang, et al.||Dec 1, 2000||290||1765-1768||hx|
|RNA editing generally refers to any process that changes the nucleotide sequence of an RNA molecule from that
of the DNA template encoding it. It has been shown that codons in some RNA ranscripts of mitochondrial
(and chloroplast) genes are altered after transcription by editing of the RNA. This paper (with two other
papers published this year: M. Higuchi et al., Nature 406, 78 (2000) and M. J. Palladino et al., Cell 102,
437 (2000).) shows this phenomenon in nuclear RNA transcription process as well. This family of nuclear
RNA-editing enzymes called ADARs (adenosine deaminases acting on RNA) convert certain adenosine bases in
an RNA transcript into inosines and thus change the protein product. These events have been shown to be
necessary for normal development of mouse and fruit fly embryos.
RNA editing has challenged the concept of faithful transmission of genetic information from DNA through
RNA to protein. Knowing the genetic sequences does not tell us everything about the protein product. :(
|NATURE||The large-scale organization of metabolic networks||H. Jeong, et al.||Oct 5, 2000||407||651-654||hx|
|The tools of graph theory and statistical mechanics are used here to quantify the metabolic networks of 43
organisms representing all three domains of life (based on data in WIT database), by means of a graph theoretic
representation of the biochemical reactions taking place in a given metabolic network (substrates as nodes,
and actual metabolic reactions as edges).
The result is stiking: all these metabolic networks have the same topological scaling properties, e.g. the degree
of interconnectivity of the network is the same for all 43 organisms, irrespective of the number of substrates
found in the given species. The networks also showed great insenstivity to random errors. It suggests that
the topology of such networks is the result of the evolutionary selection for a robust and error-tolerant
|SCIENCE||Evolution on Life's Fringes||Sep 15, 2000||289||1866-7||hx|
|The origin and evolution of viruses have not been elucidated as well as the three domains: Bacteria, Archaea,
and Eukarya. In the meeting held at sounthern France's Var region this early summer, scientists reported
some powerful new findings and new hypotheses as to these questions. The popular views hold that viruses
arose before the three domains, viruses are vestiges of bacteria that lost their cell walls and degenerated
into a parasitic existence, and viruses came from those cellular genes that somehow broke free and spun a
protein sheath. Recent work using the structure of viral genes and proteins to infer relationship between
organisms has sparked some new, provacative ideas, including the "moron accretion hypothesis" and that viruses
were important vehicles for "lateral gene transfer" in early life.
|Nature||Transmembrane phosphoprotein Cbp regulates the activies of Src-family tyrosine kinases||Kawabuchi M., et al.||4/27/2000||404||999-1003||hx|
|The membrance-associated Src family of protein tyrosine kinases (Src-PTKs) is important in the
regulation of growth and differentiation of eukaryotic cells. The Src-PTKs is inactivated by
Csk (carboxy-terminal Src kinase), which specifically phosphorylates a conserved inhibitory
tyrosine residue of Src-PTKs. Kawabuchi identified a new protein, Csk-binding
protein (Cbp), a membrane protein that brings Csk close to Src-PTK and itself is phosphorylated
by another tyrosine kinase---quite possibly an Src-PTK. The discovery of Cbp explains how the
activity of Src-PTKs, molecular switches in signal transduction pathway, is regulated.
|PNAS||Predicting ligand-binding function in families of bacterial receptors||Johnson, JM and Church, GM||April 11, 2000||97||3965-3970||shengsheng|
|Proteins with similar three-dimensional fold could have different
molecular and cellular functions. This paper talks about applying prior
knowledge of the binding-site residues to predict protein ligand-binding
functions for E. coli lactose repressor /ribose-binding proteins, and E.
coli sulfate- / phosphate-binding proteins. Strategies used here (hidden
Markov model construction, Phylogenetic and chemical reaction analysis of
binding pocket, etc. ) are applicable to other protein families.
|Current Opinion in Structural Biology||Folding and Binding||Brockwell D. et. al.||February 2000||10||16-69||hx|
|A selection of articles in this issue presents the recent attempts to study proteins fold and misfold
inside living cells, especially the involvement of molecules such as folding catalysts and molecular
cheperones, and the overall macromolecular background. It is becomeing clear that some proteins inside
cells are especially prone to various forms of aggregation and can eventually escape the diverse
cheperoning mechanisms and produce disease. Defining these events in functional and structural detail
may suggest ways to prevent such diseases.
|Nature||Rapid Degradation of a Large Fraction of Newly Synthesized Proteins By Proteasomes||Schbert U. et. al.||4/13/2000||404||770-774||hx|
|Cells make proteins with high speed but at the cost of large amounts of waste. This paper suggests that in mammalian
cells, the waste---those faulty proteins, also called defective ribosomal products (DRiPs)---may play an important
role in immune response. The authors showed that some newly produced fragments of viral protein are presented to
MHC molecules through the DRiP system which serves as a shortcut from protein synthesis to degradation.
|Structure||A new scaffold for binding haem in the cytochrome domain of the extracellular flavocytochrome cellobiose dehydrogenase||Hallberg, B.M. et al.||3/29/00||8||79-88||szhang|
|This paper described the crystal structure of the cytochrome domain of
cellobiose dehydrogenase (CDH) from fungus Phanerochaete chrysosporium.
Two unusual features have been discovered:
1. The overall fold is a beta sandwich with the same topology as the Fab
heavy chain antibody fold even thought no sequence similarity between
2. An unusual haem-binding pocket: Met and His serve as axial ligands to
hexacoordinate haem with an unusual coordination geometry.
|Science||Monitoring and Labeling Genetically Modified Products||AG Haslberger||Jan21,2000||287||431-432||Kavitha|
|A useful read for those involved in agri-biotech policy making. It has good current references on the status of EU regulations and amendments with respect to marketing genetically modified products. The new amendments seem to address increased safety provisions and risk management,transparency of regulation, and labeling of products. The article also discusses how differences in the regulatory policies in the US and Europe are having an impact on international trade, and their emerging reactions in the US.|
|Nature||Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling||Alizadeh AA, et al.||February 3||403||503-510||jhg|
This paper is a must read for anyone interested in the state-of-the-art in
large-scale, chip-based, genetic expression measurements. The authors have placed probes
for almost 18,000 different genes on a chip, the highest yet simultaneously measured, as
far as I know.
Through comparative measurements of a sample of diffuse large B-cell lymphoma patient
samples, the authors were able to make a clear distinction between patients with good
and poor prognoses. In contrast, no standard histological tests were able to distinguish
the two groups.
This paper points the way towards the implementation of large-scale molecular assays as
a standard diagnostic tool. Along with the complementary techniques for widescale
characterization of SNPs/mutations, these assays will have an enormous impact on both
diagnostic and therapeutic procedures in the near future.
|Science||Implication of Tubby Proteins as Transcription Factors by Structure-based Functional Analysis||Boggon, T.J. et al. ||12/10/99||286||2119-2125||Hongxian|
|The article presents a new approach to deduce the biochemical functions for novel proteins
through analysis of structural features. This "structure-based functional genomics" approach
demonstrates that our knowledge and understanding of biological structures has expanded to
the degree that visualizing the 3D structure of a new protein can often point the way to
biological insights. Also a novel fold, where a central hydrophobic helix at C-terminus
wholly traverses the interior of a closed beta barrel, is presented and proposed to define
a new class of DNA binding proteins.
|Nature||The language of covalent histone modifications||Strahl & Allis||01/06/2000||403||41-45||Hongxian|
|The authors describe the large network of post-translational modifications that often occur on tail domains of
histone proteins and provide attractive "histone code hypothesis" - that multiple histone modifications, acting
in a combinatorial or sequential fashion on one or multiple histone tails, specify unique downstream functions.
Undestanding the rules and the consequences of this histone code is likely to impact on many DNA-templated processes.
|Nature||Gateway to the chloroplast||Cline, Kenneth||13 Jan 2000||403||148-149||TNP|
|Review of Bauer, Kessler et.al's The major protein import receptor of plastids is essential for chloroplast biogenesis, this article details the role of the TOC complex (Toc159, Toc34 and Toc75) in chloroplast protein import. Toc159 is essential for import of proteins involved in photosynthesis while it's homologs, Toc132 and Toc120, are believed to play a role in general plastid protein import.|
|Science||Molecular Architecture of the Rotary Motor in ATP Synthase||Stock et al.||11/26/99||286||1700-1705||Hongxian|
|The article presents the structure details of membrane-embedded F0 sector in Yeast mitochondrial ATP synthase.
The electron density map provides direct proof that c protomers form a ring that is in close contact with
the gamma and delta subunits in F1 domain and supports the idea that the c oligomer is part of a rotary
motor, converting electrochemical energy into chemical energy stored in ATP. Together with another article by
Sambongi et al. in the same issue, the reports provide a coherent structural explaination for the rotary mechanism
of ATP synthesis.
|Science||Mechanical Rotation of the c Subunit Oligomer in ATP Synthase (F0/F1): Direct Observation||Sambongi et al.||11/26/99||286||1722-1724||Hongxian|
|F0/F1 ATP synthases in the mitochondria and chloroplasts of animal and plant cells, and in bacteria are the world's smallest rotary motors.
These enzymes synthesize ATP coupling with an electrochemical proton gradient and also reversibly hydrolyzes ATP to form the gradient.
The article gave the first-time observation of rotation in F0, the membrane sector and defined the molecular components of the rotary motor
of bacterial ATP synthase. This will contribute to the further understanding of the motor mechanism.
|Nature||Membrane-anchored aspartyl protease with
Alzheimer's disease beta-secretase activity||Yan. et.al.||2 Dec. 99||402||533-537||Shengsheng|
|860,000 vs 10. One good example to see how bioinformatics revolutionize traditional biology.
Beta-secretase is one of the proteases involved in the cleavage of amyloid precursor protein (APP)
in Alzheimer's disease. In searching of this enzyme, one group screened 860,000 human gene clones
(Vassar. et al.) and another group (Yan, et al., this paper) only examined 10 suspects and got the same
result. See how by reading this paper.
|Structure||Ig fold of the core binding factor a Runt domain is a member of a family of structurally and functional related Ig-fold DNA binding domains||Berardi et al.||15 Oct 1999||7||1247-1256||T.Smith|
|The combination of figures 2 and 3 in this paper provide a very nice review of the common feature
of this protein family. They also provide a great example of how the same core structure support
a wide range of auxillary component secondary structures.
|Science||DNA Topoisomerase II and Neural Development||Yang et al.||7 Jan 2000||287||131-134||Santa Fe Institue|
|It is known that in yeasts and Drosophila one type of topoisomerase is
critically important for segregation of intertwined pairs of newly
replicated chromosomes. In yeasts, the enzyme is also involved in relieving
torsional and flexural strains in DNA. It appears as one of the miracles of
molecular biology that one enzyme can be involved in different organisms in
a number of seemingly unrelated chemical processes that are in their effect
on the development of the organism highly specific.
|Nature||Structural Insights into Phosphoinositide 3-kinase Catalysis and Signalling||Walker,Edward etal.||18 November 1999||402||313-320||Kavitha|
|A "well-rounded" article which presents a clever blend of signal transduction analysis,
structural information about the mechanism of catalysis, and sequence alignment data. Hail the
power of the computational/structural dimension to enzyme kinetics research!
|Science||Pharmacogenomics (Review)||W.E.Evans and M.V.Relling||15 Oct 1999||286||487-491||tsmith|
|This article is recomended for all functional genomic's and pharmacology students.
Among other things it includes a set of very good references begining
from the late 1950's up through the 80's and 90's giving a good historic
view of the early focus on drug metaboizing enzyme polymorphisms in
humans. It has a very nice figure (fig 3 on page 490)on the micro array
analyses which lists some of the obvious genes whose expression and polymorphisms
will need to be analyzed by the industry in the next few years for most new drugs.
|Curr Opin Struct Biol||Biophysical Methods||Wider, et al.||Oct 99||9||594-648||tsmith|
|Update your knowledge! The “biophysical methods” section (8 review papers) provides good opportunity to catch up with the most recent new strategies and technical advances in X-ray crystallography, NMR spectroscopy and other methods like fiber diffraction, fluorescence microscopy. Keep an eye on Wuthrich’s TROSY technique and recent advances in automated NMR resonance assignments.|
|NAR||Heuristic approach to deriving models for gene finding||J. Besemer and M. Borodovsky||1999||27||3911-3920||tsmith|
|This is an interesting paper not only for the "gene finding" community but those interested in HMMs.
Since one of the major limitations in using HMMs is in the statistical problems associated with
training on small data sets. As some of the work in our own lab has shown often one does not have
enough data or a broad enough sample range to training for the recognition of what is biologically
anticipated. Thus this paper given a good example of an alternate approach.
|Computers & Chemistry ||Whole genome protein domain analysis using a new method for domain clustering||Gouzy, J., Corpet, F. & Kahn, D.||6/15/99||23||333-340||Hongxian|
|A systematic analysis of protein domain shuffling in 17 complete microbial genomes (12 bacteria,
4 archaea and the yeast.) The entire result (ProDom-CG) is available at
http://www.toulouse.inra.fr/prodomCG.html, where the user can navigate between sequences and domain
|JMB||Ataxia in Prion Protein PrP-deficient Mice is associated with Upregulation of the Novel PrP-like protein Doppel||Moore,R.C. et al.||Oct 1, 1999||292||797-817||TFSmith|
|The prion mystery continues! The Dpl is the first mammalain gene Homolog for PrP and its
unusual chimeric splicing may explain why some double PrP deficient mice showed no
phenotypic change! Article is a good mix of bioinformatics and solid "wet lab" molecular
|Nature||Wanted: a new order in protein nomenclature ||9/30/99||401||411||TFSmith|
|[It's about time!]
Biologists and others trying to make sense of the scientific literature have a
hard enough time keeping up with new discoveries. Inadequate attention to
nomenclature is only making the task worse.
|Nature||Genome complexity, robustness and genetic interactions in digital organisms||Lenski, R.E. et al.||12 August 1999||400||661-664||TFSmith|
|This is an interesting computer modeling study to look a selected mutation interaction
in "complex" organsims.
|Nature||Seeing a single photon without destroying it||Nogues , G. et al.||15 July 1999||400||239-242||TFSmith|
|Amazing, for all of us with some physics background this appears to violate some important aspect of good old
quantum theory --which it doesn't of course! By useing phase information only there is no violation
of the Heisenberge Uncerainty relation! Isn't Science fun?
|Protein Science||Polymer principles and protein folding ||KEN A. DILL||June 1999||V. 8 #6||1166-1180||BMERC|
|This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local &phis;psi propensities. The polymer perspective resolves two classic puzzles:
the Blind Watchmaker's Paradox that biological proteins could not have originated from random sequences, and
Levinthal's Paradox that the folded state of a protein cannot be found by random search.
|Protein Science||A Homology identification method that combines protein sequence and structure information||L. Yu, J.V. White and T.F. Smith||December 1998||vol. 7||2499-2510||BMERC|
|A study using designed (not trained) Hidden Markov Models in combination with conserved
sequence patterns. One example was the diverse serine protease family in which
the conserved pattern contained only three amino acids, the catalytic triad.
|Science||Warp speed DNA Sequencing||Joseph Alper||11 June 1999||vol. 284|| 1754||BMERC|
|A report from the May 20th annual meeting of the Biotechnology Industry Organization.
At which there were discussions of using bacterial ion channels and/or silicon-based
material pores to "pull" DNA throught while monitoring the current flow.
|Structure||Protein plasticity to the extreme||N.M. Glykos, G. Cesareni and M. Kokkinidis||15 June 1999||7||597-603||BMERC|
|A major change in the topology and helical packing of a four helical bundle with a single
amino acid substition.
|TiBS||The WD repeat: a common architecture for diverse functions||Temple F. Smith, Chrysanthe Gaitatzes, Kumkum Saxena and Eva J. Neer||May 1999||Volume 24 #5||181 - 185||BMERC|
|The WD-repeat proteins are found in all eukaryotes and are implicated in a wide variety of crucial functions.|
|Science||Sequencing the Genome, Fast||James C. Mullikin and Amanda A. McMurray||March 19, 1999||Vol. 283||1867-1868||BMERC|
|The biotechnology company Celera has generated controversy by reporting that it will sequence the
human genome in 3 years with the aid of 230 new high-throughput DNA sequencing machines, well
before the efforts of the Human Genome Project are slated to be competed. Now J. C. Mullikin and A.
A. McMurray report their evaluation of this sequencer, the ABI 3700 from Perkin-Elmer.
|Nature||Structure of a Ran-binding domain complexed with Ran bound to a GTP analogue: implications for nuclear transport||Ingred R. Vetter, Christine Nowak, Takeharu Nishimoto, Jurgen Kuhlmann & Alfred Wittinghofer||March 4, 1999||V. 398||39 - 46||BMERC|
|Ran is a small GTP-binding protein.
"...Such a mechanism represents a new type of switch mechanism and regulatory protein-protein
interaction for a Ras-related protein.
|Nature||Structure of a DNA-bound Ultrabithorax-Extradenticle hemeodomain complex||Jonathan M. Passner, Hyung Don Ryoo||Feb 25 1999||V. 397 I. 6721||714-719||BMERC|
|DNA / Protein binding.|
|Structure||The art of matchmaking: sequence alignment methods and their structural implications||Temple F. Smith||Jan 15, 1999||Vol 7 No 1||R7 - R12||BMERC|
|Proteins||Finding Local Structural Similarities Among Families of Unrelated Protein Structures||Jukka V. Lehtonen||Feb. 15||Volume 34, Number 3||341-355||BMERC|
|Cell||Molecular Bases for Circadian Clocks ||Jay C. Dunlap ||January 22, 1999||vol 96||271-290||Sean Quinlan|
|Science||Emergent Properties of Networks of Biological Signaling Pathways||Upinder S. Bhalla and Ravi Iyengar||Jan 15, 1999||Volume 283 Number 5400||381-387||Sean Quinlan|
|"Often, components of different pathways interact, resulting in signaling networks. ... These properties
of signaling networks raise the possibility that information for "learned behavior" of biological
systems may be stored within intracellular biochemical reactions that comprise signaling pathways."
|NAR||Molecular Biology Database List||Christian Burks||Jan. 1 1999||Volume 27, Issue 1||1-9||Sean Quinlan|
|Nucleic Acids Research's annual Molecular Biology Database List|
|31 Jul 1998||An Integrated Model of the
Transcription Complex in Elongation,
Termination, and Editing ||Peter H. von Hippel||7/31/98||281||660 - 665 ||Jadwiga|
|Review of the transcription mechanism|
|Science||Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete||Fraser et al. and Venter||7/17/98||281||375-388||Tom|
|The complete genome for the syphilis pathogen. Genome plots are up at: http://bmerc-www.bu.edu/bioinformatics/plots/tpallidum.html.|
|Science||Combinatorial Chemistry in Insects: A Library of Defensive Macrocyclic Polyamines||F.C. Schroeder et al.||7/17/98||281||428-431||Scott|
|Pupating beetle larvae secrete oily defensive droplets to deter insect predation. The active ingredients are macrocyclic lactones constructed from three building blocks which are apparently incorporated randomly, leading to the generation of a great variety of deterrent compounds, thereby probably evading the appearance of mutant strains of predator capable of withstanding any one compound.|
|New York Times||A Taste for Flowers Helped Beetles Conquer the World||Yoon||7/28/98||n/a||n/a||Lihua|
|Co-evolution between beetles and flowering plants. Full article in SCIENCE.|
|TIBS||Tetratrico-peptide-repeat proteins in the archaeon Methanococcus jannaschii||Kyrpides & Woese||7/28/98||23||245-247||Scott|
||N.C. Kyrpides and Carl R. Woese have identified 86 TPR (34-residue) repeats in 12 MJ proteins. Like the WD repeats they do not have a common biochemical function, but appear to mediate protein/protein interactions. The proposed fold structure is two amphipathic helices packed with "knobs-into-holes" interactions of the side chains.|
|JMB||Dynamic sequence database searching with templates and multiple alignment||Taylor||7/17/98||280||375-406||Jadwiga|
|Iterative sequence profile based search of the datatbase |
|Science||Going the Distance: A Current View of Enhancer Action||Blackwood & Kadonaga||7/3/98||281||60-63||Tom|
|Enhancer review recommended by Scott|
|Science||G Proteins and Small GTPases: Distant Relatives Keep in Touch||Hall||7/26/98||280||2074-2075||Tom|
|G-protein signalling article recommended by Temple|