Lower Sequence Research Articles

Pyroclastic deposition in the Cretaceous Shahezi Formation (Well SK‐2) Songliao Basin, China: Implications for tectonics and volcanism

Well SK‐2 is located in the Songliao Basin. Core samples from this well indicate that the Early Cretaceous Shahezi Formation has a length of 2,359.01 m and is in direct contact with the basin basement of the Middle Triassic, missing the Huoshiling Formation. This paper is focused on the lowest sequence 1 (S1, at the bottom of the Shahezi Formation, interval of 5,450.72–5,695.00 m, a length of 244.28 m) of the Cretaceous basin fills. It was found that the volcanic components contributed important parts in the sequence of basin fills, and the start of the rifting resulted from the combination of regional extensional tectonics and volcanism. Based on the centimetre‐scale description of the continuous core samples, we propose a model to delineate the interaction between tectonics, volcanism, and pyroclastic deposition. The study shows the tectonic‐volcanism in the earliest rifting stages and its control on sedimentary filling. These results also have common sense for the initial rifting process of a continental half‐graben basin. Sequence 1 of the Shahezi Formation in well SK‐2 shows a typical volcanic‐ sedimentary sequence. During the lowstand stage, the weathering‐depositional system was controlled by extension; during the transgressive and highstand stages, the transitional weathering‐depositional system and the mixed volcanic and weathering depositional system were controlled by transtension.

PPalign: optimal alignment of Potts models representing proteins with direct coupling information

BackgroundTo assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-based homology search methods, e.g. BLAST or the current state-of-the-art methods based on profile Hidden Markov Models, which rely on significant alignments of query sequences to annotated proteins or protein families. While powerful, these approaches do not take coevolution between residues into account. Taking advantage of recent advances in the field of contact prediction, we propose here to represent proteins by Potts models, which model direct couplings between positions in addition to positional composition, and to compare proteins by aligning these models. Due to non-local dependencies, the problem of aligning Potts models is hard and remains the main computational bottleneck for their use.MethodsWe introduce here an Integer Linear Programming formulation of the problem and PPalign, a program based on this formulation, to compute the optimal pairwise alignment of Potts models representing proteins in tractable time. The approach is assessed with respect to a non-redundant set of reference pairwise sequence alignments from SISYPHUS benchmark which have lowest sequence identity (between 3% and 20%) and enable to build reliable Potts models for each sequence to be aligned. This experimentation confirms that Potts models can be aligned in reasonable time (1'37'' in average on these alignments). The contribution of couplings is evaluated in comparison with HHalign and independent-site PPalign. Although Potts models were not fully optimized for alignment purposes and simple gap scores were used, PPalign yields a better mean F_1 score and finds significantly better alignments than HHalign and PPalign without couplings in some cases.ConclusionsThese results show that pairwise couplings from protein Potts models can be used to improve the alignment of remotely related protein sequences in tractable time. Our experimentation suggests yet that new research on the inference of Potts models is now needed to make them more comparable and suitable for homology search. We think that PPalign’s guaranteed optimality will be a powerful asset to perform unbiased investigations in this direction.

Carbonate platform evolution of the Tirgan formation during Early Cretaceous (Urgonian) in the eastern Kopet-Dagh Basin, northeast Iran: depositional environment and sequence stratigraphic significance

Tirgan formation of the Kopet-Dagh Basin (northeast Iran) represents one of the Urgonian carbonate platforms that were deposited during the Early Cretaceous time in the northern Alpine Tethys and deformed during the Alpine orogeny. In this study, six stratigraphic sections of the shallow-water platform sediments (Tirgan formation) were measured based on microfacies and fauna abundance. Detail study of petrography, fossil content, and sedimentary structures led to the identification of fifteen microfacies belonging to four facies belts including open marine, shoal, protected lagoon, and tidal flat. The sediments of the Tirgan formation exhibit calcareous green algae, abundant ooids, oysters, bryozoans, and crinoids in inner and middle platform ramp facies and planktonic bivalves and sponge spicules in outer-platform facies. Furthermore, the absence of basinal deposits and lack of evaporate evidence point to deposition under warm-temperate and humid climate conditions. Sequence stratigraphy analysis of Tirgan formation led to distinguish a single depositional sequence in all of the sections which are composed of transgressive and highstand systems tracts with sequence boundaries of type II (SB2). The lowermost lower Aptian Tirgan sequence in the study area relatively shows a similar trend in comparison with the global curve. This basin was deepened over time so that shaly and marly sediments of Sarcheshmeh formation were placed over Tirgan conformably and may suggest a drowning event that was likely related to unusual global warming. Last, this study contributes to the better understanding of the high distribution of facies assemblages in the Urgonian carbonate platforms.

묘곡층과 백악기 경상누층군 영양소분지 하부퇴적층의 층서와 퇴적상 분석

경북 봉화군 재산면 일대에 경상분지 영양소분지 퇴적층 산출지 북단에 소규모로 분포하는 묘곡층은 쥐라기의 대동층군과 백악기의 경상누층군을 연결하는 중요한 층서 단위임에도 불구하고 그동안 퇴적학적 연구는 매우 제한적이었다. 이번 연구에서는 이러한 묘곡층과, 영양소분지 하부 퇴적층(울련산층, 동화치층)에 대한 층서 및 퇴적학적 연구를 통해 퇴적환경과 퇴적층 발달 및 진화 과정을 제시하고자 하였다. 이번 연구에서는 야외에서 수집된 퇴적층 노두 기재 자료를 기반으로 11개의 퇴적상을 분류한 후 각각의 퇴적상을 수평 · 수직적 연장성과 산출 빈도를 고려하여 6개의 상조합으로 설정하였다. 연구 결과 묘곡층은 상조합 Ⅰ이 단일로 산출되며 호성 환경에서 퇴적된 것으로 해석된다. 울련산층은 상조합 Ⅱ와 상조합 Ⅲ이 우세하게 산출되고 있는데, 이는 간헐적으로 화산쇄설물이 공급되는 충적선상지 상부 퇴적환경에서 형성된 것으로 해석되고, 동화치층은 상조합Ⅳ와 상조합 Ⅴ가 우세하게 산출되는 퇴적층으로서 역시 간헐적으로 화산쇄설물이 공급되던 충적선상지 또는 선상지 평원과 역질 및 사질의 망상하천에서 범람원으로 전이하는 퇴적환경에서 퇴적된 것으로 해석된다. 퇴적환경 해석과 퇴적층 발달과정을 바탕으로 퇴적층 발달과정을 해석한 결과, 묘곡층은 경상분지에서 본격적으로 퇴적활동이 일어나기 전부터 이미 존재하였던 퇴적층으로 생각되는데, 부정합 관계인 묘곡층과 울련산층의 퇴적환경이 연속적이지 않는 점과 지각 운동에 의해 묘곡층 내에 수반된 여러 변형 구조들이 울련산층에는 없는 점은 묘곡층을 선경상누층군 지층으로 해석할 수 있는 근거이다.

New records of Pluteus section Hispidoderma in Turkey Based on Morphological Characteristics and Molecular Data

Twenty-six species from various sections of the genus Pluteus have been recorded from Turkey until now. In this study, phylogenetic analyses inferred from the nuclear ribosomal internal transcribed spacer (nrITS) were conducted for species delimitation and for comparisons with closely related taxa of Pluteus sect. Hispidoderma in Turkey. Our results show that P. granularis is recorded in Turkey and Europe for the first time, P. granulatus in Turkey for the first time and in Europe for the third time, P. umbrosoides in Turkey for the first time and in the world for the second time, and P. variabilicolor in Turkey for the first time. Also in this study, sequencing data for P. leoninus, P. plautus, P. roseipes, P. semibulbosus and P. umbrosus as well as the above-mentioned new records are presented for the first time from Turkey as a different geographical area. Analyses of the ITS showed that the lowest sequence divergence among in-group taxa was observed between P. semibulbosus and P. aff. semibulbosus 0.010% (SE = 0.004), the next was between P. chrysaegis and P. conizatus var. africanus 0.012% (SE = 0.004). The highest sequence divergence with in-group taxa was found between P. plautus and P. umbrosoides, 0.351% (SE = 0.039). In terms of habitat, Fagus orientalis is recorded as a new host for P. granulatus, P. granularis, P. umbrosoides, and P. umbrosus; Picea orentalis is a new host to P. granularis; Carpinus betulus for P. umbrosus; and the relict endemic Liquidambar orientalis for P. variabilicolor. Finally, this study provides detailed morphological descriptions, macro photographs and microstructure drawings relating to species of Pluteus sect. Hispidoderma from Turkey, which are rare, interesting and noteworthy. An identification key is provided for present species of Pluteus sect. Hispidoderma occurring in the country.

Закономерности размещения залежей углеводородов в берриас-нижнеаптских отложениях северных районов Западно-Сибирского осадочного бассейна

Закономерности размещения залежей углеводородов в берриас-нижнеаптских отложениях северных районов Западно-Сибирского осадочного бассейна

Molecular diagnosis of begomovirus associated with leaf curl disease of Dahlia pinnata

Diseases caused by begomoviruses represent serious threat to crop cultivation globally. A field survey was conducted in June, 2018 and severe leaf curl disease symptoms were observed on Dahlia pinnata at Ballia, U.P. India. The association of begomovirus was identified by polymerase chain reaction (PCR). The viral components were amplified by Rolling circle amplification (RCA); and digested with BamH1 and ECoRV which released the 2.7 kb fragment. The betasatellites was amplified by using betasatellites specific primers. The fragments were cloned, sequenced, analyzed and submitted to GenBank under the accession numbers (MK122994-full-length) and (MK122995-betasatellites). The full genome had total 2780 nucleotides, whereas betasatellites had 1347 nucleotides. The nucleotide sequence of full genome showed the highest identity (99.5%- 98.4%) with Tomato leaf curl Patna virus (ToLCPaV); infecting Casia tora, tomato, and Xanthium strumarium. The lowest sequence identity (37.9%) was observed with Chickpea chlorotic dwarf virus infecting X. strumarium in Pakistan. The betasatellites sequence showed the highest identity (99.2%) with Tomato leaf curl Patna betasatellites from C. tora. Currently, the association of begomovirus is known for Tomato, C. tora and X. strumarium in eastern U.P. and Bihar. Based on these findings, the begomovirus was tentatively known as a strain of ToLCPaV and designated as ToLPaV-Dahlia. This is a preliminary investigation about the natural occurrence of begomovirus causing leaf curl disease on D. pinnata in India.

Implikasi Putusan Mahkamah Konstitusi Nomor 22-24/PUU- VI/2008 terhadap Kebijakan Affirmative Action Keterwakilan Perempuan di DPRD Provinsi dan kabupaten/kota se-Daerah Istimewa Yogyakarta

The research concluded, first, The Constitutional Court decision number 22-24/PUU-VI/2008 give the positive implications of affirmative action policy of women representation in the provincial parliament and regency/town in Yogyakarta, because every legislative candidates have equal opportunity to fight to obtain a majority vote in 2009 legislative elections. Second, when Law no. 10 year 2008 still use a list of serial numbers, women’s position in the list of candidates a majority in the lowest sequence number, the result difficult for female candidates to gain seats as if his voice does not reach the number of automatic splitter sounds will be given to the serial number on it, but with a majority vote model , greater opportunities for female candidates was elected. Third, women representation in the provincial parliament Daerah Istimewa Yogyakarta (DIY) increased when compared with the results of the election of 2004, from 9 seats in 2009 elections to 12 seats, so there is an increase of 33%. in Gunung Kidul district legislature also increased the number of seats of women when compared with the acquisition of seats in the elections of 2004, from a seat in the 2009 election to 6 seats, so there is 500%. Sleman district legislature in the 2004 elections the number of women seats and as many as 6 seats in the 2009 election to 8 seats. So the increase of about 33%. in Yogyakarta city parliament also increased the number of seats in 2004 elections from 5 to 6 seats in 2009 elections. Thus, there is an increase of 20%. Kulonprogo parliament,the seats for women who gained in the 2004 elections and are 4 seats in the 2009 election into 4 seats so that there is an increase of 25%, and in Bantul Regency 2004 election results there are only 5 seats for women, in the 2009 election to 6 people or up 20%. Fourth, the concern that the ruling number 22-24/PUU-VI/2008 inhibit affirmative action policy has not been proven in Daerah Istimewa Yogyakarta (DIY), because the acquisition of women’s seats in parliament and city districts in Daerah Istimewa Yogyakarta (DIY) even more increased when compared to the acquisition in 2004 election.

GENETIC VARIABILITY OF THE REPLICASE (NIB) GENE OF PAPAYA RINGSPOT VIRUS IN NORTHERN INDIA INDICATES COMMON ANCESTRY WITH ISOLATES FROM CHINA AND TAIWAN

The purpose of the present study was to investigate the genetic variability and phylogeny of papaya ringspot virus (PRSV) on the basis of NIb (replicase) gene. The NIb and coat protein (CP) regions of about 2.5 kb of seven PRSV isolates from North India were cloned and sequenced. The North Indian isolates R2R and R5R have higher and lower sequence similarity with other PRSV isolates, respectively. Sequence comparison of NIb gene of 42 PRSV isolates, revealed that the average evolutionary divergence of all sequence pairs were 10.6% and 11.2% at amino acid and nucleotide level, respectively. Transitions were more frequent than transversions in the analyzed sequences. Maximum likelihood phylogenetic tree of combined NIb and CP regions indicated the common ancestry of North Indian isolates with Chinese and Taiwanese isolates. One potential recombination breakpoint in isolate R5R, together with its higher sequence identity and common ancestry with Chinese PRSV isolates, suggest the possible import of the former from the Chinese subcontinent.

151 COMPARATIVE ANALYSIS OF FRESH AND CRYOPRESERVED BOAR SPERMATOZOA USING RNA SEQUENCING

Fertility of cryopreserved spermatozoa is significantly reduced compared with that of their fresh counterparts, which is certainly due to the inflicted sublethal damage to spermatozoa that is observed at various molecular and cellular levels. The identification and characterisation of this damage will help us better understand sperm cryobiology and therefore develop suitable media and procedures to improve sperm cryopreservation and fertility outcomes, especially in swine. Here, we present our preliminary assessment of RNA pools of fresh and frozen‐thawed spermatozoa using RNA-sequencing technology. Semen ejaculates of 8 fertile boars were harvested and divided into 2 fractions for each ejaculate. Fraction 1 was freshly extended in commercial diluent (FD) and fraction 2 was frozen in 5-mL plastic straws (FT). Both specimens were shipped to our laboratory for analyses. The samples were purified through Percoll gradient centrifugation and resulting motile spermatozoa were washed in cold PBS. Pelleted spermatozoa were used for total RNA extraction, followed by an in-column DNase digestion. Purity and integrity of RNA samples were checked and rRNA depleted. After random priming, 40 million short cDNA reads were produced using Illumina RNA-Seq technology (Illumina Inc., San Diego, CA, USA). All reads were aligned to the pig reference genome and the produced genome-scale transcription maps consisted of both the transcript structure and the expression level of each gene mapped. Analysis of FD sperm RNA revealed a total of 18 357 sequence tags that were successfully mapped to all pig chromosomes and the mitochondrial genome. Frozen‐thawed spermatozoa showed only 16 864 sequence tags. In both FD and FT samples, chromosomes 1, 2, 6, 7, and 13 contained, in total, the highest density of mapped transcripts (>42%). Chromosome Y and mitochondrial RNAs had the lowest sequence tags mapped (<0.08%). A comparative analysis of FD and FT datasets revealed a net decrease in the total number of sequence tags (1493) with each chromosome being affected, except mitochondria. Chromosomes of FT samples showed a strong (>10%; 17, 7, 4, Y, and X) to moderate (10 to 5%) or weak (≤5%) reduction in RNA numbers. Structural annotation revealed a diverse population of sperm transcripts comprising both coding (mRNA) and noncoding (rRNA, snRNA, and mtRNA) RNAs. In both FD and FT samples, noncoding RNAs were among the most abundant sequence tags. Approximately 12 355 of sequence tags in FD v. 10 948 in FT spermatozoa were annotated with ENSEMBL and the selected genes are under investigation for comparative analyses using RT-PCR. In conclusion, mature boar spermatozoa contain a large pool of coding and non-coding RNAs that can be affected by the freezing-thawing procedure. Inflicted damage affects RNAs of all chromosomes with a great effect being seen on chromosome X. Generated datasets have the potential to lead to further study of the cryo-damage associated with reduced fertility of cryopreserved spermatozoa. Study was supported by USDA-ARS Biophotonics initiative grant # 58-6402-3-0120 and MAFES-SRI grants.

Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region

We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.

Analysis of sedimentary facies and paleo-depositional environments of the DC70X reservoir in Mbakan field of the central swamp, Niger Delta

The reservoir quality has been investigated in DC70X sandstone interval from Mbakan-6 well, Mbakan field, Niger Delta. This study involves the lithologic description and classification of 155 ft (47 m) interval of sandstone core recovered from the well. The sandstone lithofacies with their corresponding reservoir quality is strongly controlled by the paleo-depositional system. Two depositional settings are recognized in the sand-rich facies associations separated by a mudstone layer. The lower sequence consists of deposits of a prograding wave-dominated shoreface, while the upper sand consists of transgressive estuarine deposits. The deposits comprise good-quality reservoir sandstones interbedded with poor-quality reservoir sandstones, shales, and mudstones.

Genetic variability among Schistosoma japonicum isolates from the Philippines, Japan and China revealed by sequence analysis of three mitochondrial genes

The present study examined sequence variability in the mitochondrial (mt) protein–coding genes cytochrome b (cytb), NADH dehydrogenase subunits 2 and 6 (nad2 and nad6) among 24 isolates of Schistosoma japonicum from different endemic regions in the Philippines, Japan and China. The complete cytb, nad2 and nad6 genes were amplified and sequenced separately from individual schistosome. Sequence variations for isolates from the Philippines were 0–0.5% for cytb, 0–0.6% for nad2, and 0–0.9% for nad6. Variation was 0–0.5%, 0.1–0.8%, 0–0.7% for corresponding genes for schistosome samples from mainland China. For worms in Japan, genetic variations were 0–0.2%, 0.1–0.2% and 0 for the three genes, respectively. Sequence variations were 0–1.0%, 0–1.8% and 0–1.1% for cytb, nad2 and nad6, respectively, among schistosome isolates from different geographical strains in the Philippines, Japan and China. Of the three countries, lowest sequence variations were found between isolates from mainland China and the Philippines and highest were detected between Japan and the Philippines in three mtDNA genes. Phylogenetic analyses based on the combined sequences of cytb, nad2 and nad6 revealed that all isolates in the Philippines clustered together sistered to samples from Yunnan and Zhejiang provinces in China, while isolates from Yamanashi in Japan were in a solitary clade. These results demonstrated the usefulness of the combined three mtDNA sequences for studying genetic diversity and population structure among S. japonicum isolates from the Philippines, China and Japan.

Bioinformatics and Evolution of Vertebrate Pancreatic Lipase and Related Proteins and Genes

Background: Pancreatic lipase (PTL) functions in the presence of colipase in the hydrolysis of emulsified fats in the small intestine following secretion from the pancreas. Pancreatic lipase related protein 1 (PLR1) is also found in pancreatic secretions and may perform a regulatory role in lipolysis; PLR2 catalyses pancreatic triglyceride and galactolipase reactions while PLR3 may serve a related but unknown lipase function. Comparative PTL, PLR1, PLR2 and PLR3 amino acid sequences and structures and gene locations and sequences were examined using data from several vertebrate genome projects. Methods: Sequence alignments and conserved predicted secondary and tertiary structures were studied and key amino acid residues and domains identified based on previous reports on human and pig PTL. Comparative analyses of vertebrate PTL-like genes were conducted using the UC Santa Cruz Genome Browser. Phylogeny studies investigated the evolution of these vertebrate PTL-like genes. Data: Human and mouse PTL sequences shared 78% identities but only 64-68% identities with human and mouse PLR1 and PLR2 sequences. Several vertebrate PTL and PTL-like protein domains were predicted using bioinformatics including an N-signal peptide; N-glycosylation site(s); an α/β hydrolase fold region containing a catalytic triad; a ‘lid’ region for the active site; a ‘hinge’ separating the lipase and PLAT regions; and a C-terminal PLAT region. Eutherian mammalian PLR1 sequences retained residues (196Val/198Ala) responsible for the loss of triacylglycerol lipase activity whereas lower vertebrate PLR1 sequences retained the ‘active’ lipase residues. In contrast, mammalian PTL, PLR2 and PLR3 sequences exhibited lipase ‘active’ residues (196Ala/198Pro); chicken and frog PLR1 sequences retained the lipase ‘active’ residues; and opossum and platypus PLR1 sequences exhibited 196Ala/Ser198 and 196Ser/198Pro residues. A phylogenetic tree analysis provided evidence for four distinct vertebrate PTL-like gene families. Conclusions: Pancreatic lipase (PTL) and related genes and proteins (PLR1 and PLR2) are present in all vertebrate genomes examined whereas PLR3 is found only in primate genomes. The ‘inactive’ form of vertebrate PLR1 is restricted to eutherian mammals. Vertebrate PTL-like genes apparently originated in a vertebrate ancestor following gene duplication events of an ancestral PTL-like ancestral gene. Two separate lines of PTL-like gene evolution are proposed in lower vertebrates (PTL/PLR1 and PLR2), with a further gene duplication event (PLR2/PLR3) for primate genomes.

FIRST REPORT OF A BEGOMOVIRUS INFECTING MIMOSA PUDICA IN INDIA

Mimosa pudica L. (family Fabaceae) is an invasive species with ornamental and medicinal uses (Nayagam et al., 1999), native to Brazil and widespread in tropical and sub-tropical parts of the Americas, Africa and Asia, including India. The vernacular English name (touch-me-not) originates from the fact that the leaves fold inward when touched or shaken and reopen after a few minutes (seismonastic movement). During an extensive survey for whitefly-transmitted geminiviruses, samples were collected in Rajasthan (India) from stunted M. pudica plants with small and yellow leaves. The association of a geminivirus with the disease was suspected due to the presence of Bemisia tabaci (Genn.) on the plants. PCR assays using begomovirus coat protein gene-specific primers (forward 5’-ATGGCGAAGCGACCAG-3’ and reverse 5’TTAATTTGTGACCGAATCAT-3’) (Hallan, 1998), amplified a fragment 771 bp in length from symptomatic, but not from symptomless samples. The amplicons were cloned in pGEMT vector (Promega, USA), selected clones were sequenced in both orientations, and a sequence was deposited in GenBank (accession No. HQ876467). The highest nucleotide sequence identity (97%) was found with both Ageratum yellow vein virus-Guangxi (AYVV-Gx[CN:Gx13:Tom: 02], AJ558120) and [CN:Gx68:03], AJ849916) and Ageratum yellow vein virus-[G129] (AM940137). A nucleotide identity of 92% was found with both Tomato yellow leaf curl Mindanao virus and (EU487046) and Stachytarpheta leaf curl virus (StaLCuv [CN:Hn5.4:01] AJ564743). The sequences showed lower sequence identity (80%) with both Sida yellow vein Vietnam virus (SiYVVNV [VN:Han:05], DQ641696) and Papaya leaf curl China virus (PaLCuCNVPap [CN:Gx22:Tom:02], AJ704604). To the best of our knowledge this is the first published report of a begomovirus associated with Mimosa pudica in India.

Microstructure of deposits in Baer’s mounds at the lower course of the Volga River

Results of the microscopic study of sandy rocks from the Bugrovaya and lower Khvalynian sequences at the lower course of the Volga River are discussed. The terrigenous material of these deposits represents a mixture of clasts of two types: argillic (clayey) and nonargillic. The argillic component (clasts of chocolate clays) predominates in the clastic material and imparts the brownish red color to sands and sandstones of the Bugrovaya sequence. The nonargillic component includes fragments of crystals and rocks, the assemblage of which is similar to the clastic material of the underlying Khvalynian sand. The combination of clay clasts, which are not prone to long-range transport, with redeposited crystallo-and lithoclasts indicates the presence of different provenances. Their thin banding (lamination) related to differentiation of the clastic material by composition and grain size and the presence of glauconite grains testify to the aqueous origin of the Bugrovaya sequence.

Unique Substrate Recognition by Botulinum Neurotoxins Serotypes A and E

Botulinum neurotoxins (BoNTs) are zinc proteases that cleave SNARE proteins to elicit flaccid paralysis by inhibiting the fusion of neurotransmitter-carrying vesicles to the plasma membrane of peripheral neurons. There are seven serotypes of BoNT, termed A-G. BoNT serotype A and serotype E cleave SNAP25 at residues 197-198 and 180-181, respectively. Unlike other zinc proteases, the BoNTs recognize extended regions of SNAP25 for cleavage. The basis for this extended substrate recognition and specificity is unclear. Saturation mutagenesis and deletion mapping identified residues 156-202 of SNAP25 as the optimal cleavage domain for BoNT/A, whereas the optimal cleavage domain for BoNT/E was shorter, comprising residues 167-186 of SNAP25. Two sub-sites were resolved within each optimal cleavage domain, which included a recognition or active site (AS) domain that contained the site of cleavage and a binding (B) domain, which contributed to substrate affinity. Within the AS domains, the P1', P3, and P5 sites of SNAP25 contributed to scissile bond cleavage by LC/A, whereas the P1' and P2 sites of SNAP25 contributed to scissile bond cleavage by LC/E. These studies provide insight into the development of strategies for small molecule inhibitors of the BoNTs.

PETROGENESIS AND TECTONO-MAGMATIC SIGNIFICANCE OF THE ALBANIDE - HELLENIDE SUBPELAGONIAN OPHIOLITES

The Mirdita-Subpelagonian ophiolites of the Albanide-Hellenide orogen are parts of a continuous belt extending from the former Yugoslavia to Greece, and share common geological, litho-stratigraphical, geochemical, and metallogenic features. In the Albanian sector, two distinct ophiolitic belts can be clearly identified: the Western Belt, mainly composed of mid-ocean ridge (MORB) ophiolites, and the Eastern Belt characterized by supra-subduction zone (SSZ) ophiolites with prevalent island arc tholeiitic (IAT) and minor boninitic affinity. In the easternmost border of the Western Belt (Central Mirdita), a transitional zone with MORB/IAT intermediate basalts and boninitic dykes also occur. In the Greek sector, a definite distinction into two ophiolitic belts cannot be made, and MORB-type ophiolites (western type) are subordinate, being represented only by the intrusive and lower volcanic sequences of the Pindos Massif. By contrast, SSZ- ophiolites (eastern type) are predominant and well-represented by the IAT and boninitic sequences of the Vourinos Massif, as well as by MORB/IAT intermediate basaltic-andesitic suites and boninites of the upper part of the Pindos volcanic sequence. Petrological and geochemical modelling suggest that the different Albanide -Hellenide ophiolitic sequences originated from distinctly different parental magmas by partial melting of mantle sources progressively depleted by previous melt extractions. MORB may have derived from 10 - 20% partial melting of an undepleted lherzolitic source, while MORB/IAT intermediate basalts may have generated by ca. 10% of H2O-assisted partial melting of a cpx-poor lherzolite that had previously experienced MORB extraction. IAT magmas and boninites may, in turn, have derived from 10 – 20 % and ca. 30% partial melting of the same source, variably enriched by subduction-derived fluids and related incompatible elements. The favoured tectono-magmatic model for the genesis of the Albanide-Hellenide ophiolites implies a low plate-convergence velocity with: 1) intra-oceanic subduction within a pristine MORB lithosphere, resulting in SSZ magmatism with IAT affinity, and generation of a nascent arc by nearly open-system supply of undifferentiated basalts (sheeted dyke complexes); 2) progressive slab sinking and retreat coupled with mantle diapirism and extension from the arc axis to the forearc region, with generation of boninites and/or very low-Ti tholeiites from depleted sub-arc sources, leaving highly depleted harzburgitic residua; 3) contemporaneous generation at the spreading axis of IAT/MORB intermediate basalts resulting from the interference of MORB-source diapirs with suprasubduction mantle sources; 4) convergence processes leading to obduction of large and relatively intact lithospheric sections of SSZ ophiolites onto the Pelagonian continental margin, often with the interposition of metamorphic soles. The latter have prevalent MORB affinity and represent relics of the pristine MORB lithosphere overthrust by the still hot ophiolitic slab.

Mixed carbonate-siliciclastic infilling of a Neogene carbonate shelf-valley system: Tampa Bay, West-Central Florida

The shelf-valley system underlying Tampa Bay, Florida’s largest estuary, is situated in the middle of the Neogene carbonate Florida Platform. Compared to well-studied fluvially incised coastal plain valley systems, this shelf-valley system is unique in its karstic origin and its alternating carbonate-siliciclastic infill. A complex record of sea-level changes, paleo-fluvial variability and marine processes have controlled the timing and mechanisms of this ‘compound’ shelf-valley infill. A dense grid of high-resolution, single-channel seismic data were collected at the mouth of Tampa Bay, in an attempt to define this stratigraphy, determine the controls on deposition, and define the underlying structure of this shelf-valley system. The seismic data were correlated with nearby wells and boreholes for lithologic and age control. Sequence stratigraphic methods were incorporated in order to develop an integrated chronostratigraphy for the depositional infilling of the shelf-valley system. Five seismic sequences were identified. Sequence boundaries generally show erosional truncation and karstification, with downlap of overlying sequences. Structure contour and isopach maps indicate that the Tampa Bay shelf-valley system has remained in essentially the same location since its formation in the early Miocene, although the provenance of sedimentary infill has changed. This change is due to increasing amounts of siliciclastic material during the Neogene. Seismic facies interpretations indicate lower-energy, northward prograding deposition dominated by predominantly carbonate sediments within the lowest Sequence A. Higher energy, siliciclastic fluvio-deltaic deposition within sequences B and C originates to the east and northeast of the shelf-valley system related to a Pliocene pulse of sedimentation onto the Florida Platform. Finally, marine processes (longshore transport, ebb-tidal delta formation) dominate the upper two sequences (D and E), reworking these siliciclastic sediments into a spatially mixed carbonate-siliciclastic depositional setting.

Paleoenvironmental evolution of the Pliocene Villarroya Lake, northern Spain. A multidisciplinary approach

Abstract The Pliocene Villarroya basin fill consists of lacustrine and alluvial deposits over 100 m thick. The lacustrine deposits, up to 30 m thick, comprise three sequences. The two lower sequences consist of profundal, laminated deposits formed by mostly terrigenous facies that are overlain by charophytic carbonates and varves. The uppermost, third sequence made up of massive bioturbated mudstones corresponds to a very shallow lacustrine–palustrine environment. Bulk mineralogy comprises carbonates, clay minerals, quartz and feldspars. The carbonates are: exogenic, biogenic calcite and biogenic aragonite. Biogenic calcite constitutes ostracod shells and charophyte stem encrustations, whereas aragonite forms gastropod shells and, in some varve intervals, charophyte encrustations. The clay minerals are illite, kaolinite, palygorskite, chlorite and paragonite, which are inherited from source rocks, and smectite and interstratified clays, which are probably formed in the soils of the source area. Variations in clay mineralogy reflect the interplay between the climate, tectonic rejuvenation and the paleogeography of the basin. The pollen assemblages indicate significant variations in climate: a first phase of varying climate was followed by cool-temperate and sub-humid phases that culminated in a temperate and dry episode, which is recorded in the lower part of the second lacustrine sequence. This was succeeded by a marked warm and humid episode, which may be correlated with the Mid-Pliocene warmth about 3.0 Ma and the subsequent cooling phase, which is recorded in the upper, third sequence. In the two lower sequences (profundal lacustrine deposits), ostracods indicate oligosaline to mesosaline waters with salinity variations and some warm and Na–Cl episodes. Molluscs are characterized by hydrobiids, suggesting a salinity stress. In the upper, palustrine deposits, the ostracods and aquatic mollusc assemblages indicate fresh, cold waters. Faunal records indicate that changes in salinity do not correlate with climate, suggesting phases of significant saline inputs to the lake which were recorded in the lower first sequence and in the upper part of the second sequence. The lacustrine sequence of Villarroya record pronounced variations in climate and in the lacustrine environment. However, there are no consistent relationships between the climate conditions inferred from the pollen data and the sedimentary record of the environmental changes, showing that other factors, especially tectonics, have exerted an influence on the paleoenvironmental evolution, and on the sedimentary record of the Pliocene Villarroya lake.