205 research outputs found
Changes in maize transcriptome in response to maize Iranian mosaic virus infection
No full textBackgroundMaize Iranian mosaic virus (MIMV, genus Nucleorhabdovirus, family Rhabdoviridae) causes an economically important disease in maize and other gramineous crops in Iran. MIMV negative-sense RNA genome sequence of 12,426 nucleotides has recently been completed. Maize Genetics and Genomics database shows that 39,498 coding genes and 4,976 non-coding genes of maize have been determined, but still some transcripts could not be annotated. The molecular host cell responses of maize to MIMV infection including differential gene expression have so far not been elucidated.Methodology/Principal findingsComplementary DNA libraries were prepared from total RNA of MIMV-infected and mock-inoculated maize leaves and sequenced using Illumina HiSeq 2500. Cleaned raw transcript reads from MIMV-infected maize were mapped to reads from uninfected maize and to a maize reference genome. Differentially expressed transcripts were characterized by gene ontology and biochemical pathway analyses. Transcriptome data for selected genes were validated by real-time quantitative PCR.Conclusion/SignificanceApproximately 42 million clean reads for each treatment were obtained. In MIMV-infected maize compared to uninfected plants, 1689 transcripts were up-regulated and 213 transcripts were down-regulated. In response to MIMV infection, several pathways were activated in maize including immune receptor signaling, metabolic pathways, RNA silencing, hormone-mediated pathways, protein degradation, protein kinase and ATP binding activity, and fatty acid metabolism. Also, several transcripts including those encoding hydrophobic protein RCI2B, adenosylmethionine decarboxylase NAC transcription factor and nucleic acid binding, leucine-rich repeat, heat shock protein, 26S proteasome, oxidoreductases and endonuclease activity protein were up-regulated. These data will contribute to the identification of genes and pathways involved in plant-virus interactions that may serve as future targets for improved disease control.</div
Diamond v. Chakrabarty: Oil Eaters: Alive and Patentable
No full textCongress is empowered, under article I, section 8 of the United States Constitution, to create patent laws that encourage the promotion of arts and sciences. In the congressional fulfillment of this task, the courts have been confused as to what products are worthy of patent protection under the patent statutes. One illustration of this confusion is the recent controversy of whether living organisms fit into the statutory patentable classification of section 101 of the 1952 Patent Act. The recent United States Supreme Court decision of Diamond v. Chakrabarty has ended this confusion by holding that living micro bacteria is patentable as a manufacture or composition of matter under section 101. The author makes an exhaustive survey of the areas of confusion surrounding interpretation of the patent statutes and analyzes the Chakrabarty decision from the perspective of resolving these areas of confusion. The author ultimately agrees with the decision, but notes that although the confusion in this area is abated, the controversy still remains
Typhleotris mararybe Sparks & Chakrabarty 2012, new species
No full text<p> <i>Typhleotris mararybe,</i> new species</p> <p>Figures 7C, 9–10; table 1</p> <p>HOLOTYPE: AMNH 245601, 44.2 mm SL; Grotte de Vitane (Vitany), sinkhole near Itampolo, coastal plain below and to west of Mahafaly Plateau, southwestern Madagascar, 24°42′07.1″S, 043°57′51.3″E, MAD-1-2008, coll. J.S. Sparks, P.W. Willink, P. Chakrabarty, and S.B. Holtz, 5 June 2008. Hologenetypes CytB, COI, and ND1 (following the nomenclature of Chakrabarty, 2010a) are available on GenBank under accession numbers JQ619660, JQ619665, and JQ619670, respectively.</p> <p>PARATYPE: AMNH 245602, 37.9 mm SL, data as for holotype.</p> <p> DIAGNOSIS: The new species is characterized by uniformly dark brown pigmentation throughout the body, and extending onto the fins for 1/3 of their length; only the distal 2/3 of each fin lacks pigment, apart from the dorsal fins, which are dark brown (vs. an all white body and fins in both congeners). In addition, <i>T. mararybe</i> can be distinguished from congeners by the presence of prominent and protruding anterior skeletal elements. Protruding lateral ethmoid, sphenotic, and pterotic projections, in combination with a strongly sunken and concave orbital region, lend the head a sculpted and angled bony appearance (vs. relatively smooth and more or less fleshy in congeners), particularly in dorsal view (figs. 7C, 9), a shorter pectoral fin not reaching a vertical through the anus when adpressed (vs. pectoral fin extending to anus in congeners), and an elevated vertebral count (26 vs. 25 or fewer in congeners). The new species is further distinguished from <i>T. madagascariensis</i> by the absence of scales fully covering the head (vs. head fully scaled in <i>T. madagascariensis</i>) and a longer second predorsal length (64.9%–69.0% vs. 56.2%–64.1% in <i>T. madagascariensis</i>), and from <i>T. pauliani</i> by a shorter prepelvic length (33.0%–33.9% vs. 34.1%–40.4% in <i>T. pauliani</i>), a pelvic formula of I, 5 (vs. I, 4 in <i>T. pauliani</i>), and the absence of a single leading spine in both the second dorsal and anal fins (vs. leading spines present in <i>T. pauliani</i>).</p> <p>DESCRIPTION: Selected proportional measurements and meristic data presented in table 1. Based on the specimens available, a small (<45 mm SL), elongate (BD <25% SL) and overall thin gobioid. Body wide anteriorly and head dorsoventrally compressed, particularly rostrally. Head bony, and sculpted in appearance, not fleshy, rounded, and smooth. Toothed margins of both upper and lower jaws visible externally when mouth closed. Inside of mouth white. Mouth large, and gape wide. No eyes. Snout and anterior portion of head elongate and shovellike, with a bony, armored appearance, creating a duck-billed appearance. Body becoming progressively laterally compressed posteriorly. Caudal peduncle laterally compressed, shallow, and elongate. Anterior nostril small, tubular, located near upper lip; posterior nostril short, somewhat slitlike and fleshy, but opening more or less oval. Numerous deep canals present on dorsal, lateral, and ventral surfaces of head; canals lined with numerous small pores.</p> <p>Oral jaw teeth small, recurved, and conical; teeth numerous and arranged in six or seven closely set and irregular rows anteriorly in both upper and lower jaws. Teeth tapering to fewer rows of somewhat smaller teeth posteriorly, as well as medially proximal to synthesis, where tooth rows become noticeably reduced in number and constricted, in both upper and lower jaws. Teeth present along full length of premaxillary arcade and dentary. Porelike structures present on basihyal (tongue).</p> <p>Nine or 11 thin, elongate, triangular, and medially denticulate gill rakers arrayed along lower limb of first arch. Epibranchial rakers on first arch of similar morphology, numbering four in holotype.</p> <p> Head asquamate, except scales extending anteriorly onto roof of neurocranium and also covering operculum (note: in paratype ctenoid scales extend onto the cheek and comprise about 4–6 columns; no scales extending onto cheek in holotype, i.e., anteriorly terminate on operculum). Although scales on top of head do not extend nearly as far forward as in <i>T. madagascariensis</i>, squamation does extend to anterior margin of neurocranium, but scales do not extend anteriorly onto snout (as in <i>T. madagascariensis</i>). Otherwise, body fully scaled to the caudal fin, including chest region anterior to the pelvic fin and inner margin of pectoral fin. Cycloid scales present ventrally on chest and belly. Scales cycloid on body, except operculum, which is covered with strongly ctenoid scales. All other scales on body appear to be cycloid. Scales arranged in irregular rows, uneven in size, with smallest on roof of head and largest on operculum. Fleshy pectoral base covered with ctenoid scales. Pectoral-fin axil asquamate.</p> <p>Two dorsal fins. First dorsal fin with five spines and second dorsal fin with eight rays. Anal fin with eight rays. Pelvic-fin origin anterior to vertical through origin of pectoral fin and slightly anterior to vertical through distal margin of opercle. Pectoral fin with 14 or 15 rays. Anus located anterior to vertical through anterior insertion of second dorsal fin. First dorsal fin small, spines feeble, and located posterior to vertical through pectoral-fin origin. Urogenital papilla small, not reaching anal fin when adducted. Pelvic fin short. Pectoral fin elongate, but not reaching level of urogenital papilla when adducted. In congeners pectoral fin extends well posterior of urogenital papilla when adducted. Caudal fin short and slightly rounded distally. Vertebral count 26.</p> <p>COLORATION AND PIGMENTATION PATTERN IN LIFE AND ALCOHOL (figs. 9, 10): Body uniformly dark brown. All fins dark brown proximal to base, whereas distal 2/3 of caudal, pelvic, pectoral, and anal fins depigmented and white. First and second dorsal fins more or less dark brown. In alcohol, the white coloration on the distal portion of the fins becomes an opaque off-white, whereas the dark brown base coloration of the body remains more or less unchanged.</p> <p> ETYMOLOGY: From the Malagasy <i>marary</i> (“ill or sick”), and <i>be</i> (“big”), meaning “very sick” or “big sickness” in reference to the strange debilitating viral illness or “sinkhole fever” members of our team contracted after snorkeling in Grotte de Vitane. The specific epithet, <i>mararybe,</i> is to be treated as an adjective.</p> <p> DISTRIBUTION AND HABITAT (figs. 1, 11): The type locality and only known habitat of <i>T. mararybe</i> is Grotte de Vitane (S: 24°42′07.1″; E: 043°57′51.3″), which is a sinkhole located near the town of Itampolo on the coastal plain below and to the west of the extensive, more or less north-south running, Mahafaly Plateau. Grotte de Vitane (fig. 11) is a karst formation with nearly vertical walls, whose water level at the time of our survey was approximately 10–15 m below the rim. The diameter of the sinkhole was approximately 100 m across at its widest, and 70 m at its narrowest, with more or less shear walls. The height of the sinkhole walls to the water level was approximately 50 m on its southern end, and much shallower on the northern end (approximately 20 m).</p> <p>A chain ladder was used to climb down into the sinkhole to access the water where approximately five specimens of the new species were observed (fig. 11B). In a nearly four-hour effort, two of these fish (the holotype and paratype) were captured by the first author using a small hand net while snorkeling. The two specimens were collected at or near the surface of the water, and dove straight down when approached. Another member of our group (P. Willink, FMNH, now at Shedd Aquarium) was able to observe additional individuals while snorkeling, but no additional specimens could be collected at the time of the survey.</p> <p> Interestingly, in contrast to most other collection localities for <i>Typhleotris</i>, in which the water is generally quite shallow, the water in Grotte de Vitane was uniformly deep. At the time of collection (early June), the water was relatively clear, deep, and warm. Via several dives to inspect the substrate for fishes by the first author, it is estimated that the water level in the sinkhole was about 7.5–10 m deep on average. Although the water was clear, much suspended large particulate material was present in the water column. Apart from the new species of <i>Typhleotris</i>, the sinkhole water included an abundance of aquatic invertebrates, including water scorpions (Nepidae), shrimp, and water spiders. It is also interesting to note that all of the specimens observed, including those collected, were swimming in open water within 1–1.5 m of the surface. Upon being chased, all individuals immediately dove toward the bottom.</p> <p>A portion of Grotte de Vitane is exposed to full sunlight, and there is a short (1 m) undercut shelf along the otherwise sheer walls that was not directly exposed; however, the dark, subterranean portion of this particular system extended much further than one could snorkel on a breath of air, and remains unknown. Although we only encountered a few individuals in the sinkhole, all were darkly pigmented and blind. Given that portions of the sinkhole receive direct sunlight, possession of uniformly dark brown body coloration may function to camouflage individuals from predators or offer protection from UV radiation.</p> <p> REMARKS AND COMPARISONS: <i>Typhleotris mararybe</i> can be distinguished from <i>T. madagascariensis</i> by the absence of scales on the anterior part of the head (compare figs. 2, 6A, and 7A with figs. 7C, and 9–10). Both <i>T. pauliani</i> and <i>T. mararybe</i> have scales extending only up to the roof of the neurocranium, not fully covering the cheek and orbital region (the paratype of <i>T. mararybe</i> and a single individual of <i>T. pauliani</i> were observed to possess a few scales on the cheek anterior of the operculum, with scales covering only the posteriormost portion of the cheek), or extending onto the anterior portions of head (i.e., anterior half of frontals or snout); <i>T. madagascariensis</i> has a fully scaled head. Although all three described species of <i>Typhleotris</i> are scaled along the ventrum anterior to the pelvic fin, these scales are both weakly ossified, compared to other body scales, and highly embedded in both <i>T. madagascariensis</i> and <i>T. pauliani</i>, making them quite difficult to discern in preserved material.</p> <p> It is possible that the initial mention of the new species described herein was a consequence of a hydrological survey of the southwestern region of Madagascar (Guyot, 2002). Guyot (2002) notes that he encountered small blind fish, which he determined to be <i>Typhleotris madagascariensis</i>, at several locations on the Mahafaly Plateau. In reference to the locality named “F16” in his dissertation and referred to as Vintany sinkhole, Guyot (2002: fig. IV-2 and table IV-2) mentions that the fish appeared within the fluid expelled through drilling efforts. No further mention was made regarding the fish, nor was any description presented. According to information available to us through our guides, however, Vintany sinkhole (S: 24°02′37.6″; E: 043°45′19.6″) is located in the vicinity of Mitoho Cave, near Lake Tsimanampetsotsa and within Parc National de Tsimanampetsotsa. Vintany sinkhole did indeed yield depigmented and blind specimens referable to <i>T. madagascariensis</i> (table 1). The sinkhole near Itampolo where we collected the new pigmented species is called Grotte de Vitane (Vitany) (S: 24°42′07.1″; E: 043°57′51.3″), which seems to better match the placement of Guyot’s (2002) Vintany sinkhole, according to his rather vague maps; however, given the limited data provided, we cannot be certain.</p> <p> As discussed above, Grotte de Vitane is connected to an underground system of water via subterranean passages, but it is unclear whether the new species survives there. The dark brown pigmentation of <i>T. mararybe</i> makes them inconspicuous against the similarly dark background of the sinkhole walls and appears to provide effective camouflage. We hypothesize that the presence of a darkly pigmented blind species in an environment with significant exposure to direct sunlight is the result of this species being derived from a subterranean blind species that invaded this new habitat (Chakrabarty et al., 2012). As with other <i>Typhleotris</i>, individuals of the new species are relatively slow swimmers, but reacted quickly, diving toward the bottom when chased by our nets. It should be noted that individuals of <i>T. pauliani</i> were observed to move away from an approaching object with much more energy than <i>T. madagascariensis</i>.</p> <p>Notably, Grotte de Vitane is regarded as a sacred site frequented by locals for prayer; the locals are apparently unaware that fish inhabit the sinkhole. Some locals are capable of using tree roots to lower themselves in and out of the sinkhole, but seemingly do this infrequently. For all of the other localities we sampled with cavefishes, local villagers were generally aware of the existence of these populations, which include all known blind fish localities in Madagascar discovered to date.</p> <p> Both <i>T. madagascariensis</i> and <i>T. pauliani</i> are listed as “Endangered” in the IUCN Red List of Threatened Species (Loiselle et al., 2004). Accordingly, given the extremely circumscribed distribution of the new species, a single small sinkhole that is easily accessible, coupled with its rarity in that fragile habitat, we believe that <i>T. mararybe</i> should also be listed as threatened.</p>Published as part of <i>Sparks, John S. & Chakrabarty, Prosanta, 2012, Revision of the Endemic Malagasy Cavefish Genus Typhleotris (Teleostei: Gobiiformes: Milyeringidae), with Discussion of its Phylogenetic Placement and Description of a New Species, pp. 1-28 in American Museum Novitates 2012 (3764)</i> on pages 16-23, DOI: 10.1206/3764.2, <a href="http://zenodo.org/record/4598002">http://zenodo.org/record/4598002</a>
. = Chakrabarty hoy: a 30 años de la Resolución de la Corte Suprema norteamericana.
No full textChakrabarty today: 30 years after the United States Supreme Court ResolutionThe decision of the United States Supreme Court in the Chakrabarty case marked the beginning of a far reaching process, the development of which considerably extended the field of patentability of humans, their body parts and genetic information. The author believes that a period of three decades is sufficient to draw conclusions. A critical point has been reached from a debatable decision, which had more economic support than legal, which requires serious recapitulation of the scope and the purpose of industrial property rights
Arsenic in Rice: A New Global Disaster
No full textRice (Oryza sativa L.) is amidst the great essential food crop that offers a staple food for most
of the world’s populace. Arsenic (As) is a carcinogenic heavy metal, which harms human
health. In Asian countries, a major source of human As-intake is rice grains and; contamination
of paddy soils by As and accumulation of As in rice grains is one of the serious agricultural
issues. Hence, it is important to mitigate the effects of As toxicity as much as possible. In
an attempt to minimize As accumulation in grains various genes have been introduced in
rice. The main objective of this review is to provide an overview of the arsenic problem and
various biotechnological methods exploited for reducing As accumulation in rice grain.</jats:p
Editorial: Molecular mechanisms of metal toxicity and transcriptional/post-transcriptional regulation in plant model systems
No full textAdjustment of the Auxiliary Variable(s) for Estimation of a Finite Population Mean
No full textIn this paper we have worked to weight and transform various estimators by Prasad (1986) and Lui (1991). We have introduced some ratio and ratio type estimators under weighting, transformation and model based approach, environment. We have introduced estimators efficient than estimators proposed by Chakrabarty (1979), Singh and Singh (1997), Singh (2002) and Singh et al. (2006).model based approach; percent relative efficiency; product estimator; ratio estimator; regression estimator; simple mean unit estimator
Climate change in a critical planetary perspective: Dipesh Chakrabarty and the Anthropocene vs. Capitalocene controversy
No full textThe essay traces Dipesh Chakrabarty’s reflections on the Anthropocene, the epoch of “anthropogenic” climate change, to discuss them in light of the critiques developed in ecomarxist circles, particularly by Jason W. Moore, Andreas Malm, and Alf Hornborg. Chakrabarty, a well-known exponent of postcolonial studies and keen critic of globalization processes, points out that the “globe” of “globalization” is not the same “globe” of “global warming,” but rather “the planet” – the Earth-system – with its many forms of life. A complex trajectory of deliberation leads the author to question the “geological agency” of human beings and, ultimately, argue that the climate crisis can be better understood and addressed from a “planetary perspective" (rather than a humanocentric one) capable of placing “life in general” at the center of discussion. In their critiques of the Anthropocene narrative, Moore, Malm, and Hornborg speak instead of a “Capitalocene.” Through comparison with this critical stance, the essay highlights and discusses some of the theoretical premises underpinning Chakrabarty’s thinking so as to advance the hypothesis of a critical planetary perspective. Such a perspective recognizes capitalism as an ecological regime and climate change as a political challenge in which the problem of human domination over the rest of nature is clearly intertwined with the problem of domination and privilege in interhuman relations
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