Bogidiella indica, A New Species of Subterranean Amphipod Crustacean (Bogidiellidae) from Wells in Southeastern India, with Remarks on the Biogeographic Importance of Recently Discovered Bogidiellids on the Indian Subcontinent

Bogidiella indica, new species, is described from three water wells in southeastern India, including a bore-well on the campus of Acharya Nagarjuna University in Nagarjunanagar, a water well in Guntur town, and an agricultural well in the Godavari and Krishna Basin, all in the state of Andhra Pradesh, India. The new species is assigned to the genus Bogidiella Hertzog and to a newly designated species group within the genus. Despite the near circum-global distribution of the family Bogidiellidae, only a single, partially intact specimen of a bogidiellid had been collected from the Indian subcontinent prior to the discovery of specimens from the well in Nagarjunanagar. Including the new taxon described in this paper, the family Bogidiellidae contains 35 genera and 106 species. Although B. indica is closely similar to other species presently assigned to the genus Bogidiella, it is easily distinguished by a proportionately shorter and relatively heavily spinose pereopod 5. The sexes are generally similar except that the male bears a large, distally modified apical spine on the inner ramus of uropod 1. The location of the well sites within 45 to 50 km of the eastern coast of India strongly suggest that they lie in an area that was submerged under shallow marine water within the last 1 million years

Relative toxicity of neem to natural enemies associated with the chickpea ecosystem: a case study

Neem products are often perceived as harmless to natural enemies, pollinators and other non-target organisms. For this reason, several integrated pest management (IPM) programmes have adopted neem as one of the prime components. This study revealed toxic effects of neem on soil-inhabiting and aerial natural enemies in chickpea to an extent of 41 and 29% population reduction, respectively, compared with 63 and 51% when using a conventional insecticide (endosulfan). Neem also affected the parasitization of Helicoverpa armigera (Hu¨ bner) larvae by Campoletis chlorideae Uchida up to 20%. The natural enemy population started building up from the vegetative phase and reached their peak during the reproductive phase, and there was a gradual decline from pod formation to pre-harvest phases of the crop. Adapting the currently used IPM system in chickpea using neem during the vegetative phase, followed by an application of Helicoverpa nuclear polyhedrosis virus (HNPV) at flowering and need-based application(s) of chitin inhibitors like novaluron or flufenoxuron instead of endosulfan during pod formation would strongly augment natural enemy populations. This paper discusses the relative toxicity of neem and other IPM components on soil-inhabiting and aerial natural enemies in the chickpea ecosystem

Understanding Helicoverpa armigera pest population dynamics related to chickpea crop using neural networks

Insect pests are a major cause of crop loss globally. Pest management will be effective and efficient if we can predict the occurrence of peak activities of a given pest. Research efforts are going on to understand the pest dynamics by applying analytical and other techniques on pest surveillance data sets. We make an effort to understand pest population dynamics using neural networks by analyzing pest surveillance data set of Helicoverpa armigera or Pod borer on chickpea (Cicer arietinum L.) crop. The results show that neural network method successfully predicts the pest attack incidences for one week in advance

Integrated Pest Management (IPM) for Reducing Pesticide Residues in Crops and Natural Resources

Investigation on the pesticide residues during 2006–2009 in various crops and natural resources (soil and water) in the study village (Kothapally, Telangana State (TS)) indicated the presence of a wide range of insecticidal residues. Pooled data of the 80 food crop and cotton samples, two rice grain samples (3 %) showed beta endosulfan residues, and two (3 %) soil samples showed alpha and beta endosulfan residues. In vegetables of the 75 tomato samples, 26 (35 %) were found contaminated with residues of which 4 % had residues above MRLs. Among the 80 brinjal samples, 46 (56 %) had residues, of these 4 % samples had residues above MRLs. Only 13 soil samples from vegetable fields were found contaminated. The frequency of contamination in brinjal fields was high and none of the pulses and cotton samples revealed any pesticide contamination. IPM fields showed substantial reduction sprays which in-turn reflected in lower residues. Initial studies on water analysis indicated the presence of residues in all water sources with higher in bore wells compared to open wells, however, by 2009 the water bodies reflected no residues above the detectable level

Synthesis and Investigation of a Radioiodinated F3 Peptide Analog as a SPECT Tumor Imaging Radioligand

A radioiodinated derivative of the tumor-homing F3 peptide, (N-(2-{3-[125I]Iodobenzoyl}aminoethyl)maleimide-F3Cys peptide, [125I]IBMF3 was developed for investigation as a SPECT tumor imaging radioligand. For this purpose, we custom synthesized a modified F3 peptide analog (F3Cys) incorporating a C-terminal cysteine residue for site-specific attachment of a radioiodinated maleimide conjugating group. Initial proof-of-concept Fluorescence studies conducted with AlexaFluor 532 C5 maleimide-labeled F3Cys showed distinct membrane and nuclear localization of F3Cys in MDA-MB-435 cells. Additionally, F3Cys conjugated with NIR fluorochrome AlexaFluor 647 C2 maleimide demonstrated high tumor specific uptake in melanoma cancer MDA-MB-435 and lung cancer A549 xenografts in nude mice whereas a similarly labeled control peptide did not show any tumor uptake. These results were also confirmed by ex vivo tissue analysis. No-carrier-added [125I]IBMF3 was synthesized by a radioiododestannylation approach in 73% overall radiochemical yield. In vitro cell uptake studies conducted with [125I]IBMF3 displayed a 5-fold increase in its cell uptake at 4 h when compared to controls. SPECT imaging studies with [125I]IBMF3 in tumor bearing nude mice showed clear visualization of MDA-MB-435 xenografts on systemic administration. These studies demonstrate a potential utility of F3 peptide-based radioligands for tumor imaging with PET or SPECT techniques

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2–4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity

The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were converted into separate sets of Boolean features, depending on the absence or the presence of variants in each gene. An ensemble of LASSO logistic regression models was used to identify the most informative Boolean features with respect to the genetic bases of severity. The Boolean features selected by these logistic models were combined into an Integrated PolyGenic Score that offers a synthetic and interpretable index for describing the contribution of host genetics in COVID-19 severity, as demonstrated through testing in several independent cohorts. Selected features belong to ultra-rare, rare, low-frequency, and common variants, including those in linkage disequilibrium with known GWAS loci. Noteworthily, around one quarter of the selected genes are sex-specific. Pathway analysis of the selected genes associated with COVID-19 severity reflected the multi-organ nature of the disease. The proposed model might provide useful information for developing diagnostics and therapeutics, while also being able to guide bedside disease management. © 2021, The Author(s)

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Chilibathynella kotumsarensis Ranga Reddy, n. sp.

<i>Chilibathynella kotumsarensis</i> Ranga Reddy n. sp. <p>(Figs 2–6)</p> <p> <i>Etymology</i></p> <p>The specific epithet alludes to the type locality of the new species.</p> <p> <i>Type locality</i></p> <p>The Kotumsar Cave, a limestone cave, is one of the largest caves in India. It lies on the bank of the River Kanger, flowing through the Kanger Valley National Park (18º52'09" N; 81º56'05" E), at an altitude of 560 m near Jagdalpur town, Bastar District, Chhattisgarh State, India (Fig. 1).</p> <p>The cave entrance is a vertical fissure in the wall of a hill. It has a narrow, twisted opening, measuring about 15 m in length. The cave is honeycombed in its structure, consisting of several irregular chambers. The main tunnel of the cave is nearly 500 m long and has several lateral and downward passages. The roofs and walls of the different chambers are lined with colorful dripstone formation, resulting from the precipitation of calcite-dissolved carbonate lime. The chambers are floored with either rocks or pebbles of varying dimensions or surface-derived soil/clay deposits.</p> <p>Some of the abiotic parameters of the cave, as determined by Pati & Agrawal (2002), between May 1987 and March 1988, were as follows: air and water temperatures remained relatively stable, at an annual average of 28.25 ± 1.23 ºC and 26.33 ± 0.96 ºC respectively (range = 25.0–32.7 ºC for air; 22.9–29.3 ºC for water). The water pools were alkaline, with an annual average pH of 8.04 ± 0.36. Conductivity peaked during December, with an annual average of 0.27 ± 0.03 m Mhos. The annual mean for dissolved oxygen and percentage saturation for oxygen in the cave water were 6.42 ± 0.52 mg /l and 74.83 ± 5.91%, respectively. The cave is subject to frequent flooding during monsoon activity, which generally begins in the middle of June.</p> <p>.</p> <p> <i>Material examined</i></p> <p>Holotype, adult male, dissected on four slides. Paratypes, adult male, dissected on four slides, and four juveniles, one of them dissected on two slides, three mounted as whole specimens on a single slide. Type material has been deposited in the National Museum of Natural History, Paris; registration numbers: holotype MNHN-Sy 16 (male); paratypes: MNHN-Sy 17 (male), MNHN-Sy 18 (1 juvenile), MNHN-Sy 19 (3 juveniles). Leg. Y. Ranga Reddy, 0 1 December 2004.</p> <p> <i>Diagnosis</i></p> <p>Parabathynellid of small size (1.25 mm). Antennal organ small, represented by two contiguous dentate structures. Fifth antennular segment with two aesthetascs. Antenna sixsegmented. Thoracopod I with well-developed epipodite. Pleopod I with two setae. Uropodal sympod with inhomonomous row of spines. Uropodal exopodite with three setae, two apical and one lateral, and endopodite without spines. Anal operculum convex.</p> <p> <i>Description of male (holotype)</i></p> <p>Total length 1.25 mm (male paratype 1.28 mm). Body elongate, maximum width at first abdominal segment. Abdominal segments wider than thoracic ones. Head 25% longer than wide and slightly longer than first three thoracic segments combined.</p> <p> <i>Antennule</i> (Fig. 2 d) consisting of seven, somewhat elongate, slender segments, 29% longer than head; length of first three segments only slightly exceeding that of last four segments. First segment longest, 1.7 times longer than wide, with two dorso-medial, simple setae near distal margin; two dorsal plumose setae at about distal outer corner, one tiny seta at distal inner corner, and one plumose seta on sub-distal outer margin. Second segment with two dorsal and one ventral simple setae near distal inner angle; antennal organ much reduced, represented by two conical, dentate and nearly contiguous hyaline structures; one plumose and one simple seta on sub-distal outer margin, one dorsal, plumose seta near distal outer corner, and one ventral plumose seta close to mid-outer margin. Third segment with one seta at sub-distal outer margin and one ventral and one dorsal seta near distal inner corner. Inner flagellum of third segment slightly longer than wide, with three simple setae. Fourth segment with three plumose setae, two unequal setae on the tip of apophysis and one at its base on outer side; apophysis reaching about proximal third of fifth segment. Fifth segment with two aesthetascs and two simple setae dorsally. Sixth segment longer than seventh one and with three aesthetascs and four setae dorsally. Seventh segment with three aesthetascs and four setae.</p> <p> <i>Antenna</i> (Fig. 3 a) six-segmented (basal additional segment, if any, is not discernible with the optics used); right one curved backwards, bending between third and fourth segments; left one nearly straight, antero-laterally directed, 0.7 as long as antennule; percentage lengths of segments 1–6 as follows: 5:13:20:16:19:27; segments 1 and 4 without seta; segments 2, 3, 5, and 6 with 1, 2, 1, and 4 (3 apical and 1 lateral) setae, respectively.</p> <p> <i>Labrum</i> (Fig. 3 b,c) flat, symmetrical, free margin straight, bearing eight main, nearly uniform teeth and 1 smaller marginal tooth on each side (N. B. Unfortunately, the labrum was folded in permanent preparation of the holotype as in Fig. 2 b).</p> <p> <i>Mandible</i> (Fig. 3 d,e): distal part of <i>pars incisiva</i> with 4 teeth, tooth of the ventral edge small and pointed. <i>Pars molaris</i> (”Borstenlobus”) with 8 claws, of which the distal two smooth, relatively large, forming a separate group; other claws with fine denticles on proximal margins; proximal outer corner of <i>pars molaris</i> with a row of spinules. Palp onesegmented, about three times as long as wide, bearing a terminal seta, slightly exceeding <i>pars incisiva</i> in length.</p> <p> <i>Maxillule</i> (Fig. 3 f) with two endites; proximal endite small, somewhat oval in outline, with four apical claw-like spines, distalmost one longest. Distal endite bending inward, gradually tapering posteriad and with two terminal and four inner marginal claws. Outer distal margin with three simple setae.</p> <p> <i>Maxilla</i> (Fig. 3 g) consisting of four segments. First segment with an elongately oval endite, carrying two elongate plumose and two short simple setae. Second segment with six (four inner-marginal, two medial) and third segment with 13 setae. Fourth segment tiny, with one claw and three setae.</p> <p> <i>Thoracopods</i> I–VII (Figs 4 a–d, 5a–c) well developed; length gradually increasing from pairs I–III. Thoracopods III–VII almost similar in size. Thoracopods I–VII each bearing one-segmented epipodite on coxa and one inner marginal seta on basis. Exopodite one-segmented, with two unequal terminal setae; an additional subterminal seta present on dorsal side of thoracopod V alone (see Variation). Endopodite four-segmented. First and second endopodal segments of thoracopods I–VII with a rudimentary seta each at distal outer corner (not considered for setal formulae). Setal formulae:</p> <p>Thoracopod I: 2 + 0/2 + 0/2 + 0/3(1)</p> <p>Thoracopod II: 1 + 0/ 1 + 0/1 + 0/3(1)</p> <p>Thoracopods III–IV: 1 + 0/ 1 + 0/0 + 0/3(1) Thoracopods V–VII: 0 + 0/ 1 + 0/0 + 0/3(1)</p> <p> <i>Thoracopod</i> VIII (Fig. 5 d, e) massive, characteristic in shape. Basal segment of protopodite large, oblong, juxtaposing basis and originating at the same level as the basis. Dentate lobe shorter than the rounded inner lobe and with straight or somewhat convex free margin, carrying five or six teeth in a row. Basis roughly conical, extending well beyond the level of dentate lobe and with one subapical seta. Epipodite (external lobe) conical and arising from the basis. Exopodite curved, sharply bending backward and with a row of apical denticles. Endopodite rectangular, with one subapical and two unequal apical setae.</p> <p> <i>Pleopod</i> I (Fig. 5 f) one-segmented, nearly four times as long as wide, with one long apical and one short subapical seta.</p> <p> <i>Uropod</i> (Fig. 2 a). Sympod more than twice the length of endopodite and 4.6 times longer than its own maximum width, with eleven spines, distalmost spine largest and smooth; all other spines acutely pointed, almost similar in size and with serrulate lateral margins. Exopodite almost cylindrical, 5.4 times as long as wide, measuring 52% of sympodite length and bearing two apical setae, each with a row of spinules at base, inner seta twice as long as outer seta, and one short seta at about distal third of outer margin. Endopodite somewhat dagger-shaped, reaching 41% of sympodite length; bearing two unequal plumose setae at about the middle of outer margin and two equal plumose setae medially; spinules occurring on distal outer margin and on inner margin, as illustrated.</p> <p> <i>Pleotelson</i> (Fig. 2 a) with one seta on either side near the base of furcal ramus; seta bare, shorter than furcal ramus. Anal operculum broadly triangular in outline, with rounded tip (Fig. 2 b).</p> <p> <i>Furcal rami</i> (Fig. 2 a) 36.5% longer than maximum width, maximum width occurring at proximal third, outer margin nearly straight and ending in large, blunt ventral projection (furcal organ) (Fig.2 c), distal two-thirds of inner margin expanded, with two terminal and five inner, pointed, serrulate spines and two unequal dorsolateral setae; terminal spine largest and with a row of dorsal spinules at its base, other spines gradually decreasing in size, as illustrated.</p> <p>Female: Not known.</p> <p> <i>Description of juveniles</i> (Fig. 6 a–e)</p> <p>Four sexually undifferentiated juveniles were recorded.</p> <p>Juvenile 1 (Fig. 6 a, b): Total length 0.96 mm. Body eight times longer than wide. Head 24% longer than wide. Antennule 29% longer than head. Habitus and the various structural details of the cephalic appendages, thoracopods I–V and pleopod I are as in the adult. Sixth and seventh thoracic segments with rounded sternum in lateral view (Fig. 6 b), but without any trace of thoracopods. Thoracopod VIII represented by an undifferentiated, triangular lobe. Anal operculum slightly projecting backwards, somewhat rectangular in outline and depressed at the middle. Furcal rami with only six spines, the largest spine of the adult rudimentary, in the form a short, filamentous structure. Uropod as in the adult except for the sympod carrying seven spines, distal most spine largest.</p> <p>Juveniles 2 and 3 (Fig. 6 c, d): Total length 0.83 mm. Both are identical to each other and differ from the juvenile 1 in two respects: thoracopod VIII is a very small crescentic lobe, and pleopod 1 is absent.</p> <p>Juvenile 4 (Fig. 6 e): Total length 0.78 mm, similar to juveniles 2 and 3 except for the absence of any trace of thoracopod VIII.</p> <p> <i>Va r i a t i o n</i></p> <p>The number of spines borne by the uropodal sympod varies between 9 and 11 in the adults and, 5 and 8 in the juveniles. The exopodite of thoracopod V has one dorsal seta in the holotype whereas it is absent in the male paratype as well as juveniles. The anal operculum is different between the adults and juveniles. No variation has been noticed in the armature of caudal furca.</p>Published as part of <i>Reddy, Y. Ranga, 2006, First Asian report of the genus Chilibathynella Noodt, 1963 (Bathynellacea, Syncarida), with the description and biogeographic significance of a new species from Kotumsar Cave, India, pp. 23-37 in Zootaxa 1370</i> on pages 25-32, DOI: <a href="http://zenodo.org/record/174899">10.5281/zenodo.174899</a&gt